[med-svn] [r-cran-r.utils] 07/13: New upstream version 2.6.0
Andreas Tille
tille at debian.org
Thu Nov 9 13:18:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-r.utils.
commit 3a323ae7099ecfa33bf74f6bbc9facd9e06fe8af
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 9 14:06:47 2017 +0100
New upstream version 2.6.0
---
DESCRIPTION | 11 +-
MD5 | 92 +-
NAMESPACE | 1 +
NEWS | 3372 ++++++++++++++++++++++++++-----------------
R/compressFile.R | 6 +-
R/fileAccess.R | 3 +-
R/findSourceTraceback.R | 2 +-
R/gcDLLs.R | 17 +-
R/intToBin.R | 103 --
R/intToHex.R | 145 +-
R/intToOct.R | 22 -
R/isEof.connection.R | 7 +
R/isSingle.R | 2 +-
R/loadObject.R | 14 +-
R/loadToEnv.R | 16 +-
R/nullfile.R | 2 +-
R/reassignInPackage.R | 4 +-
R/shell.exec2.R | 2 +-
R/use.R | 4 +-
R/withCapture.R | 31 +-
R/withLocale.R | 8 +-
R/withOptions.R | 8 +-
R/withRepos.R | 8 +-
R/withSeed.R | 8 +-
R/withSink.R | 8 +-
R/withTimeout.R | 39 +-
man/as.character.binmode.Rd | 2 +-
man/compressFile.Rd | 6 +-
man/fileAccess.Rd | 3 +-
man/gcDLLs.Rd | 8 +-
man/intToBin.Rd | 22 +-
man/isEof.connection.Rd | 7 +
man/isSingle.Rd | 4 +-
man/loadToEnv.Rd | 2 +-
man/nullfile.Rd | 2 +-
man/reassignInPackage.Rd | 4 +-
man/shell.exec2.Rd | 2 +-
man/use.Rd | 5 +-
man/withCapture.Rd | 10 +-
man/withLocale.Rd | 4 +-
man/withOptions.Rd | 4 +-
man/withRepos.Rd | 4 +-
man/withSeed.Rd | 4 +-
man/withSink.Rd | 5 +-
man/withTimeout.Rd | 59 +-
tests/intToHex.R | 55 +-
tests/withCapture.R | 4 +
tests/withTimeout.R | 35 +
48 files changed, 2578 insertions(+), 1608 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index e1293bc..c7b15dd 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,9 +1,9 @@
Package: R.utils
-Version: 2.5.0
-Depends: R (>= 2.14.0), R.oo (>= 1.20.0)
+Version: 2.6.0
+Depends: R (>= 2.14.0), R.oo (>= 1.21.0)
Imports: methods, utils, tools, R.methodsS3 (>= 1.7.1)
Suggests: digest (>= 0.6.10)
-Date: 2016-11-07
+Date: 2017-11-04
Title: Various Programming Utilities
Authors at R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email = "henrikb at braju.com"))
@@ -14,7 +14,8 @@ License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://github.com/HenrikBengtsson/R.utils
BugReports: https://github.com/HenrikBengtsson/R.utils/issues
+RoxygenNote: 6.0.1
NeedsCompilation: no
-Packaged: 2016-11-07 15:58:57 UTC; hb
+Packaged: 2017-11-04 17:21:15 UTC; hb
Repository: CRAN
-Date/Publication: 2016-11-07 21:07:28
+Date/Publication: 2017-11-05 15:03:17 UTC
diff --git a/MD5 b/MD5
index 56897bb..0aede68 100644
--- a/MD5
+++ b/MD5
@@ -1,6 +1,6 @@
-c004b0eeef4311f24774eb61e8764c95 *DESCRIPTION
-4e7ad060c1f2fcbc990f594f1945d95d *NAMESPACE
-1a355ee8784dc181292ff8bbf396c61e *NEWS
+a2fc3fc7aabbb97caad25d4b735689a5 *DESCRIPTION
+c9674eaef3a8d87648fee971faeff1f2 *NAMESPACE
+eb4ae7fd70a3e82f9fdb63499afa54c9 *NEWS
5b3e0291bcc049d9ada9005162c5259a *R/000.R
58ba1d04831f66b31ab3f48026b64a80 *R/006.fixVarArgs.R
78609173e9b93e07864506d108bb8adb *R/999.NonDocumentedObjects.R
@@ -37,7 +37,7 @@ f542e11cf867c672c759df91d0a56afa *R/captureOutput.R
14ade0c1e02f89384988accd7a396673 *R/cmdArgs.R
c3d3114a3bbcefe5444fdfe5fc4707c1 *R/colClasses.R
c74d4c1fadceabdacd1da595dffbf306 *R/commandArgs.R
-4a76b7df6ec0897dbafc187959132ec7 *R/compressFile.R
+61b5836163d68b0546cafbd3ba88aa19 *R/compressFile.R
da04a6dd9ddb45f15f127dc63c1304c3 *R/compressPDF.R
fce9ee80742085ad12d6146c5c69d106 *R/copyDirectory.R
958e23aaf32c067a7a7e31285196fdf8 *R/copyFile.R
@@ -60,12 +60,12 @@ e8cfd9acf4c09722a6774ec7781c4670 *R/displayCode.R
40c70d164da025d0e08ede12a0fb5af9 *R/egsub.R
d0a52423f7a2239eaf2652f6c235b209 *R/env.R
3c57e5b6cc281e9ff596b20b79388416 *R/extract.array.R
-c4faca747d899d6957ad4a7544acecac *R/fileAccess.R
+8db13198bc7c80f83ff360f41f2b8586 *R/fileAccess.R
03a6f721c22e04a8871b6b120d84fc95 *R/filePath.R
712f0e82e99b0f3dfc8958f062387c7c *R/finalizeSession.R
3952d91b9891bc7e09d1bea92080ba17 *R/findFiles.R
-bad6097f7f66a08d196f2e38171d19e8 *R/findSourceTraceback.R
-73afaa0e3c4c634238e60fb82a3d4634 *R/gcDLLs.R
+80ad88f0c67301fa89f04fdbf0ab4f76 *R/findSourceTraceback.R
+f1f02f1456b65880e73fe81c899a5bc4 *R/gcDLLs.R
2448aab75b234f3f95a31b2d232b6843 *R/gcat.R
5dcbd930fb01d9390ecaa1d3772ee0ba *R/getAbsolutePath.R
912c7aea7f65b9507ffc141421f40463 *R/getCommonPrefix.R
@@ -79,25 +79,23 @@ f3944a47daa518896ebc150459a44057 *R/hsize.R
d435ed49272712bb9af5a886adddc2d5 *R/inAnyInterval.R
aa3bdfeb2d480acbd3f20a9825682db1 *R/insert.R
5c1c4bd24f0fe489caa23f02da342129 *R/installPackages.R
-8c38a0cfb75be7a9b4bbe557988b4682 *R/intToBin.R
-bea184cfe85ef716d2dabfebf6435b7f *R/intToHex.R
-85577887b460a7573293b7b99f5a8cf5 *R/intToOct.R
+1d9d020267bcd713b11d59616733d188 *R/intToHex.R
09ddf1006e7e1f4ea17d213f389dbb27 *R/intervalsToSeq.R
6c5b30494d71d6fa1165ac1c7605ca9b *R/isAbsolutePath.R
803e9b08213b7a27c5650c8295ae8b98 *R/isDirectory.R
-123e5ffda65092ecd185e9229c831de1 *R/isEof.connection.R
+59ec70f0497cc0887c4941fd88fd65e7 *R/isEof.connection.R
da8e4906da7257c81f0686a129d958a5 *R/isFile.R
77b49be1302f490737563d8e2614e417 *R/isOpen.character.R
0ed6329369fdf3ad0e5c3d55214d064c *R/isPackageInstalled.R
776f17ca0c32be022825a5ea1ebb1ccc *R/isPackageLoaded.R
344969d029dab41654298a3198b1cbd8 *R/isReplicated.R
-d2b281b988abe8e1ec65eed052d4b637 *R/isSingle.R
+93f348313a26cf25466acec5d691221b *R/isSingle.R
bcae426199760661336022bef90632d5 *R/isUrl.R
681d8a7cb2b0a50542e3f49486d4d0df *R/isZero.R
b27653b09203f3faf66808afa3594fd5 *R/lastModified.R
e9c6b1c6ca75b025912f826385fe0a5b *R/listDirectory.R
-5806dc9a894ccc57386ead09dc1a1434 *R/loadObject.R
-94bad650890af0816d620df25199ef78 *R/loadToEnv.R
+1a58ddc8e966b6889015b34dd2f51e3d *R/loadObject.R
+40c0a7072fd9f2f47358c78621e00de5 *R/loadToEnv.R
0b45fa0531b07008809128e536aff2b8 *R/mapToIntervals.R
61bd82cb58cceadf4b62880b7eff19c2 *R/mergeByCommonTails.R
84b91adaf1894c10cc70cee8b015a075 *R/mergeIntervals.R
@@ -105,7 +103,7 @@ e9c6b1c6ca75b025912f826385fe0a5b *R/listDirectory.R
9d19f292520cbf6a06401b2a7d101f7d *R/mout.R
49a413624da591bab31ea8e1901c5527 *R/moveInSearchPath.R
7dc693a2fba955e2e1c09e934039dac8 *R/mpager.R
-bfa635869e5adf0029990efd203f85db *R/nullfile.R
+ec7d44f57d6b46413f50427287556604 *R/nullfile.R
5678be9f44191f2b9b7b3adb1634a425 *R/onGarbageCollect.R
6f9d623c303edc888550db35db943706 *R/onSessionExit.R
6b995e49ff2535cf200db6f28c91ea1b *R/parseArgs.R
@@ -122,7 +120,7 @@ fda2fda1be856ac65d8c013d4305b715 *R/readRdHelp.R
ed7bf2b4da491befe5771acbfaecd8f3 *R/readTableIndex.R
692dacdce0acc8f3636f6643bd86ad72 *R/readWindowsShellLink.R
d7ed8804b2fc13020c253c0d0940c947 *R/readWindowsShortcut.R
-c79953f34203fc3688fed95d1238e12e *R/reassignInPackage.R
+7fb7049249873f590dc6052122952ed0 *R/reassignInPackage.R
a338e1b90fc1a60fb3d0671dfff0f7d8 *R/removeDirectory.R
2638cef880d4aba655b6fdb46bbc0ea2 *R/renameFile.R
7c802705c094b4439fcc0d3ab73008d4 *R/resample.R
@@ -131,7 +129,7 @@ a338e1b90fc1a60fb3d0671dfff0f7d8 *R/removeDirectory.R
3d3be841aab4a54e4cf1df5b49ddc3c6 *R/seqToHumanReadable.R
3b1c9d01dc366df2a3d829dff4b3a3b9 *R/seqToIntervals.R
a99c43fede37d2ec8e0205cf9c575aa1 *R/setOption.R
-f99c0d985c39c13f90a36919cb4add8a *R/shell.exec2.R
+db114f20ac04c374be35dca594907b50 *R/shell.exec2.R
4d08eb6b51aad08255b28222c1efd474 *R/sourceDirectory.R
906e401ba7c001e0049fc2191b04ebbe *R/sourceTo.R
9eb78bc76cbd1fe187f3f57ac1412c15 *R/splitByCommonTails.R
@@ -146,16 +144,16 @@ aa80c8d708db45d566e12d25c551f210 *R/toAsciiRegExprPattern.R
9be946c174218311182bd7d5b87aef7a *R/toUrl.R
2002fcc6cb2211f086fa4605fc7ac06b *R/touchFile.R
1ec2122c792a96e27d6cdafa4f5a3102 *R/unwrap.array.R
-b65318b81f38e9c381c21893b15e7ce8 *R/use.R
+00b7e0b2884813f498a6804675cd5553 *R/use.R
e6715bde6eeb47c0912cad8a2a481104 *R/useRepos.R
cc957386e356fde41d58d9b5fe40e92d *R/whichVector.R
-f66c89a164d19e407305d1eace413843 *R/withCapture.R
-3501e1cb5cbba1091d8a9606b923b3ad *R/withLocale.R
-b2e7fe514a3157c42f8cf2d66b500869 *R/withOptions.R
-5e54a8056d1118e3871db6d39a309331 *R/withRepos.R
-668140561964b6d58aad555a7a273e7e *R/withSeed.R
-1f192c5d894b529bb9b24f791cfe5dfe *R/withSink.R
-d27d690455911c04c5f067401309ee97 *R/withTimeout.R
+35bb24aeed7454b7f715063ff8fea079 *R/withCapture.R
+1c3746a2f092652921e8b7e8a59bdfb4 *R/withLocale.R
+d32e924b51c12ed1bb7576c625ce409c *R/withOptions.R
+7e0d90758b17f17b42c391b9fb2c4f8e *R/withRepos.R
+e670c59e2424e6c1497579b04d797617 *R/withSeed.R
+ce5fd858a86bee2795ca9bb863455236 *R/withSink.R
+b1275185b4b48f2cc1f8fb7e1abf9815 *R/withTimeout.R
7d76ba24b1578834dc5e27a71e21a767 *R/wrap.array.R
f821ed391718f9ef19aedf9cbf0a2c26 *R/writeBinFragments.R
45ebae49ea75312675a0f6c3b2014bc8 *R/writeDataFrame.R
@@ -190,7 +188,7 @@ c366c029b7c251644fcf76d5821a535b *man/addFinalizerToLast.Rd
dfa29f5299da734576c2b9ef81322646 *man/as.character.Options.Rd
a1dfac301e5392c6bf76a2ca63f460ed *man/as.character.ProgressBar.Rd
4e58c75b8e908562aaea2bae326eb920 *man/as.character.Verbose.Rd
-67a56edf91f80d354d34010a07407326 *man/as.character.binmode.Rd
+c472d6154cf9bb2f4173e9585a28f88b *man/as.character.binmode.Rd
1ee83d26a7bfef402e8772bb5f5ee5d1 *man/as.double.Verbose.Rd
4274a2ee6e785c512d9af83566694ff6 *man/as.list.MultiVerbose.Rd
4393d45c6ee5267b1a91d60c67a4cea1 *man/as.list.Options.Rd
@@ -213,7 +211,7 @@ f31acaefc8030e38057f4e0026fdd36e *man/cmdArgs.Rd
2b685382ce094ecf0b8389638c364684 *man/colClasses.Rd
0500e010c3466b8c4dea4f3677c4416b *man/commandArgs.Rd
3e3efb3735bd0edbbfae7c96c159bf14 *man/compile.SmartComments.Rd
-3af48796249feadd14a6c306e685b458 *man/compressFile.Rd
+bf8fb080b9d7fb40cf522f67b3a29be5 *man/compressFile.Rd
b242af88983f5705acf5c4dc1986da00 *man/compressPDF.Rd
a11749b463ff39b65939fb934bdd96c0 *man/convertComment.SmartComments.Rd
9e3d14b2f1f94b72ccceddf2e83361cb *man/convertComment.VComments.Rd
@@ -242,7 +240,7 @@ a20873e3799b53f3bb03ad9cc5c18933 *man/evaluate.GString.Rd
a27608db1b994303687d7cfe9f42178c *man/exit.Verbose.Rd
71205565a290410adae12a3382feb4f7 *man/extract.array.Rd
ab73bbf146cf6162f26542c99ceef785 *man/file.info2.Rd
-ebc0100382c3f0674a95650f1e1f95a8 *man/fileAccess.Rd
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f8e41fb41e3a616693d8043c56b2674d *man/filePath.Rd
c296c9f5490cc0d0b1bcf0656e24dd71 *man/finalizeSession.Rd
f4ee85ca8d88cad81baa9fd8a5619dd8 *man/findFiles.Rd
@@ -251,7 +249,7 @@ d9fdcda02532eb85dfcd2f6ef4c9366d *man/findGhostscript.System.Rd
d53cb36d56dc8042605e707be691ddf4 *man/findSettings.Settings.Rd
e3360522cedf16319063f909cb167359 *man/findSourceTraceback.Rd
5ff260dbc288c4821c477c5eb26d6c93 *man/flush.TextStatusBar.Rd
-b13254c8a75ea8d94cbcbae0c7f437bf *man/gcDLLs.Rd
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33f85d47eabdf0e0ecc1b21a14e85048 *man/gcat.Rd
afd5299bc4c69c3b8aada2ab0d846ea6 *man/getAbsolutePath.Rd
957b30ec9f988eb20cc249c12268d7ab *man/getBarString.ProgressBar.Rd
@@ -303,12 +301,12 @@ ec33c72104299c98f17524bcde17cb85 *man/hsize.Rd
81a242d2e3fb0c04d4d5c7ad9b02c639 *man/inherits.Assert.Rd
991e66ed91e50a0ad1fda8b49fd6aef6 *man/insert.Rd
bb78772298e99f8c313e7fa9f1c80cb7 *man/installPackages.Rd
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f8b69a0a4afa099b1ff0d7890c1c6745 *man/intervalsToSeq.matrix.Rd
de0d54f119c661059750a615283dd60a *man/isAbsolutePath.Rd
8ed02e65889d3ae432bed7b400085bf4 *man/isDirectory.Rd
11a67bdd46e3b6c5cb9e200d1fa53626 *man/isDone.ProgressBar.Rd
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2cafbcb295eb367e1c41c1a54e8bc1a7 *man/isMatrix.Assert.Rd
aa9b98c472e10dbd372121cafecf281a *man/isModified.Settings.Rd
@@ -319,7 +317,7 @@ fd07008f20f2068c0b1b085a405c62c1 *man/isPackageInstalled.Rd
85c02449e8e99dd399806c16d8c51208 *man/isPackageLoaded.Rd
67aeaaf34b378fd8d3fdf50fcd58e0cd *man/isReplicated.Rd
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8d64987abac7766467bb6186a3ee4fb9 *man/isUrl.Rd
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@@ -330,7 +328,7 @@ a636c3ab5dee6ee62da4033155a7855b *man/less.Verbose.Rd
cab3ca0a0527d00f83c86b314c3e4924 *man/listDirectory.Rd
3134ae47e6d8b5d7fe4f8b60a1f1e2f1 *man/loadAnywhere.Settings.Rd
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6e51be00789219f57bfdeb217240c3a4 *man/mergeIntervals.numeric.Rd
0d75be48d7ec0e0e171fa3f63c6d4033 *man/mkdirs.Rd
@@ -342,7 +340,7 @@ ccb8fa039832c94293bd803c04dfa111 *man/moveInSearchPath.Rd
861f03d04270f6f7d5043e25eb061284 *man/nbrOfOptions.Options.Rd
9c62d7ad633f32bf453755c0538ad7d0 *man/newline.TextStatusBar.Rd
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19e5fcda8159fa72aa7304551482d783 *man/on.Verbose.Rd
8b497ba57251b526cec0e05b4aacf737 *man/onGarbageCollect.Rd
@@ -374,7 +372,7 @@ a238fcea6b6984892277ccfd267fdae1 *man/readRdHelp.Rd
287e4c3c098dbf34d81b98437e0ac414 *man/readUTF.Java.Rd
c1697fab420f61ab76ebb0b0ea6498e9 *man/readWindowsShellLink.Rd
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958c68a482b02a3bc8d5a59374a0b80a *man/resample.Rd
@@ -399,7 +397,7 @@ ea957410cbc7cf0c1aeda6c527cc7e78 *man/setStepLength.ProgressBar.Rd
4bc859d15df948bfdf27b9cb4d22b598 *man/setTicks.ProgressBar.Rd
98146ae96fd66418a9ea75ad949a386c *man/setTimestampFormat.Verbose.Rd
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a1e0c2bb204f7bb4a4ef6eee47067bec *man/splitByPattern.Rd
@@ -422,19 +420,19 @@ bf20f527399595dd701853cd15b99ac6 *man/tmpfile.Rd
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6af991e15355e4853892834bfcf8e192 *man/validate.VComments.Rd
affbf2850e9d0b97998f16310e427a33 *man/warnings.Verbose.Rd
8f4153c14340aae30b3485ef32eaf8a7 *man/whichVector.logical.Rd
-96b57ca6c28ed406c197c2aef651cec0 *man/withCapture.Rd
-28604774e49827358065cae6752f6f52 *man/withLocale.Rd
-1e8621390e63fc41b33a4b8763863858 *man/withOptions.Rd
-30ab0b171a7276c0073074136fcb074f *man/withRepos.Rd
-70947d003a5a61774b4aa13c930717b0 *man/withSeed.Rd
-7c34006be56a4a6550f23b27be2cf2b4 *man/withSink.Rd
-dd15b40635c24e5cca882b06f8bf61a9 *man/withTimeout.Rd
+d10ef16cc45db74a943e11874de7c89e *man/withCapture.Rd
+5cfc890f51bf3fe3bbdf6aca06578ee8 *man/withLocale.Rd
+cfac4c6bb8b67b623ce487e1b5e7b5fc *man/withOptions.Rd
+044754db05680d00f554eaf04ddb6105 *man/withRepos.Rd
+31070b962135b28902c2fc8d182caa4c *man/withSeed.Rd
+2f1c064fbdb63579f8923b01047f56a7 *man/withSink.Rd
+abd9877923de1bfecff480ae0404ae20 *man/withTimeout.Rd
327a8fe4c7082fd9f2f088e9a906cd26 *man/wrap.array.Rd
e748a256e5c8fd1154b5547d3f4672d0 *man/writeBinFragments.Rd
937af8b9679438990e355f6d2e18c8cf *man/writeByte.Java.Rd
@@ -492,7 +490,7 @@ ae291e4a8ccaca5bbfe9ae9151cee1cb *tests/gcDLLs.R
748b1fa844820112d8ce3069569ec2ec *tests/getParent.R
303f84b13d4dc0676ff2799a3a3c4f23 *tests/hpaste.R
97f62d3f67c58879d36a4ccfbb2e7870 *tests/insert.R
-30e8c419ebdbcadf486ae91fbd3c03bd *tests/intToHex.R
+7ab249c5082fcee89795aa69a9d4942d *tests/intToHex.R
8e30d7476c7b3d5d9b3fd71fff8b6f3a *tests/isPackageLoaded.R
89964abb17f81be3ee68f1430f4ff1ba *tests/isReplicated.R
df6848e2c00461c1937db1bb1a8640c5 *tests/isUrl.R
@@ -527,13 +525,13 @@ e069d9d0afbf1988d8f99d092ba5fbe9 *tests/tmpfile.R
93d83736c757cc2bc70f51fae175a35e *tests/use.R
3b31277725c97bc3d57491a7ea990f0e *tests/useRepos.R
2958c72c21b285b370aabc0258a008c4 *tests/whichVector.R
-f84c962029616ee42bfaf0b129889d87 *tests/withCapture.R
+03ee55aa0908facbc5c881159accc294 *tests/withCapture.R
ed0c9f673fbd73d7c17a2bc0fb578b7b *tests/withLocale.R
43e6f6324ed9ccb7ecbe1f318f165e9f *tests/withOptions.R
56057cbbed2a851c3bab969e991bc7ec *tests/withRepos.R
a259831ae25761c17fc1f55684cc67e7 *tests/withSeed.R
777ac19bf7bcb0029d73aa110e14aaaa *tests/withSink.R
-9dc3b9552d17762f6b3d9829bd2d4874 *tests/withTimeout.R
+3d2b94928eb7d8ea834740642960fd55 *tests/withTimeout.R
0a21c267f7140a0def8f3976d53e0a98 *tests/wrap.array.R
661f34b3ba0beea1b45e9dff64aea177 *tests/writeDataFrame.R
84ed613188920118b43ffce5cf1432e6 *tests/zzz_finalizer_crash.R
diff --git a/NAMESPACE b/NAMESPACE
index 4c4978d..cacf55e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -282,6 +282,7 @@ S3method("update", "FileProgressBar")
S3method("callHooks", "function")
# GenericSummary
+S3method("[", "GenericSummary")
S3method("c", "GenericSummary")
S3method("print", "GenericSummary")
diff --git a/NEWS b/NEWS
index c124451..1a8b853 100755
--- a/NEWS
+++ b/NEWS
@@ -2,1957 +2,2693 @@
Package: R.utils
================
+Version: 2.6.0 [2017-11-05]
+
+NEW FEATURES:
+
+ o Argument 'install' of use() now defaults to option 'R.utils.use.install',
+ which in turn defaults to environment variable 'R_R_UTILS_USE_INSTALL'.
+ If neither is set, the default is TRUE.
+
+ o ROBUSTNESS: Now gcDLLs() runs the garbage collector before removing stray
+ DLLs in order for any finalizers who rely on the DLL to be called before the
+ DLL is removed.
+
+ o loadObject() and loadToEnv() give more informative error message if an
+ error occurs while reading from a file / connection.
+
+ o All withNnn() functions gained argument 'substitute' making it possible to
+ pass an expression object, e.g. withTimeout(expr, subsitute = FALSE, ...).
+ The expection is withCapture(), where, the now deprecated (see below),
+ argument 'substitute' means something else for legacy reasons.
+
+BUG FIXES:
+
+ o withTimeout() would produce a regular error but not a TimeoutException
+ for timeouts reaching the _total_ CPU time limit while it would work
+ for those reaching the _elapsed_ CPU time limit. Thanks to Alexej Gossmann
+ at Tulane University for troubleshooting and provide a fix.
+
+ o findSourceTraceback() could fail and give an obscure error when for instance
+ the 'XML' package was attached. It now tries a bit harder to locate the
+ internal 'srcfile' object.
+
+ o Forgot to register S3 method `[`() for GenericSummary.
+
+ o intToOct() would convert to hexadecimals.
+
+ o intToBin() would output garbage for negative values.
+
+DEPRECATE AND DEFUNCT:
+
+ o Argument 'substitute' of withCapture() has been renamed to 'replace'.
+ Code that calls withCapture(..., substitute = ...) will still work, but
+ the use of 'subsitute' is deprecated and will later become defunct.
+ The purpose of this change of argument name is so that the meaning of
+ 'substitute' can be harmonized with the other withNnn() functions.
+
+ o Deprecated evalWithTimeout(); use withTimeout() - the preferred name.
+
+
Version: 2.5.0 [2016-11-07]
-o CLEANUP: Removed operator `%<-%` which was defunct since 2.4.0.
- An alternative is to use ditto of the future package.
-o CLEANUP: Made resetWarnings() defunct.
-o BUG FIX: withCapture(x <- 1L) would drop integer suffix 'L' from
- the output when run in non-interactive mode.
+BUG FIXES:
+
+ o withCapture(x <- 1L) would drop integer suffix 'L' from the output when run
+ in non-interactive mode.
+
+DEPRECATE AND DEFUNCT:
+
+ o CLEANUP: Removed operator `%<-%` which was defunct since 2.4.0.
+ An alternative is to use ditto of the future package.
+
+ o CLEANUP: Made resetWarnings() defunct.
+
Version: 2.4.0 [2016-09-13]
-o Added strayDLLs() and gcDLLs() to identify and unload stray DLLs
- that was left behind by packages that have already been unloaded.
-o Added nullfile().
-o Now setThreshold() for Verbose accepts also logical values.
-o CLEANUP: Argument 'absolutePath' for Arguments$getReadablePathname()
- was renamed to 'absolute'. For backward compatibililty, the old
- name will still work for some time.
-o CLEANUP: Defunct `%<-%` in favor of `%<-%` in the future package.
-o Package now formally requires R (>= 2.14.0) released Oct 2011.
-o CLEANUP: Deprecated arrayIndex(). arrayInd() in base (>= 2.11.0)
- provides the same functionality.
+NEW FEATURES:
+
+ o Added strayDLLs() and gcDLLs() to identify and unload stray DLLs that was
+ left behind by packages that have already been unloaded.
+
+ o Added nullfile().
+
+ o Now setThreshold() for Verbose accepts also logical values.
+
+ o Argument 'absolutePath' for Arguments$getReadablePathname() was renamed to
+ 'absolute'. For backward compatibililty, the old name will still work for
+ some time.
+
+DEPRECATE AND DEFUNCT:
+
+ o CLEANUP: Defunct `%<-%` in favor of `%<-%` in the future package.
+ o CLEANUP: Deprecated arrayIndex(). arrayInd() in base (>= 2.11.0)
+ provides the same functionality.
+
+CODE REFACTORING:
+
+ o Package now formally requires R (>= 2.14.0) released October 2011.
+
+
Version: 2.3.0 [2016-04-13]
-o Added hsize().
-o Added tmpfile() for creating temporary files with content that
- is deleted automatically by the garbage collector unless there
- is a reference to it in R.
-o ROBUSTNESS: Now compressFile() and decompressFile(), and therefore
- also functions such as gzip() and gunzip(), output atomically
- by writing to a temporary file which is only renamed when completed.
-o CLEANUP: Deprecated `%<-%` in favor of `%<-%` in the future package.
-o Package now formally requires R (>= 2.14.0) released Oct 2011.
+NEW FEATURES:
+
+ o Added hsize().
+
+ o Added tmpfile() for creating temporary files with content that is deleted
+ automatically by the garbage collector unless there is a reference to it.
+
+ o ROBUSTNESS: Now compressFile() and decompressFile(), and therefore also
+ functions such as gzip() and gunzip(), output atomically by writing to a
+ temporary file which is only renamed when completed.
+DEPRECATE AND DEFUNCT:
+
+ o CLEANUP: Deprecated `%<-%` in favor of `%<-%` in the future package.
+
+CODE REFACTORING:
+
+ o Package now formally requires R (>= 2.14.0) released Oct 2011.
+
+
Version: 2.2.0 [2015-12-09]
-o loadObject() and saveObject() gained argument 'format' in order
- to support also RDS files (in addition to XDR files). File
- formats XDR and RDS are supported. The default format is
- inferred from the filename extension. If this is not possible,
- then the XDR format is assumed (default; backward compatible).
-o mkdirs() gained arguments 'mustWork' and 'maxTries'.
-o seqToHumanReadable() gained argument 'tau'.
-o R.utils::commandArgs() now also ackowledges 'argv' set by the
- littler executable.
-o R.utils::commandArgs() recognizes more reserved command-line
- arguments, e.g. --debugger-args=N, --min-vsize=N and --min-nsize=N.
-o ROBUSTNESS: Now writeDataFrame(..., sep, quote=FALSE) asserts
- that none of the columns contains the field separator 'sep',
- because then the written file would be corrupt/invalid.
-o ROBUSTNESS: Explicit import of all 'graphics', 'grDevices',
- 'stats' and 'utils' functions.
-o DOCUMENTATION: Clarified in help for compressFile() et al. that
- these functions remove the input file by default after the output
- file is generated. Thanks to Ben Bond-Lamberty (Pacific Northwest
- National Laboratory) for pointing out this potential pitfall.
-o CLEANUP: Deprecated resetWarnings().
-o BUG FIX: seqToHumanReadable(c(1:2, 4:5)) gave "1-2, 4, 5".
-o BUG FIX: withTimeout() did not work in non-English locales.
- Thanks to Arnaud Malapert at University Nice Sophia Antipolis for
- reporting on this.
-o BUG FIX: GString ignored "simple" attributes, e.g. $[tolower]{y}.
- Thanks to Andre Mikulec for reporting on this.
-o BUG FIX: downloadFile() via https://<user>:<pwd>@<domain>/ gave
- an error.
+NEW FEATURES:
+
+ o loadObject() and saveObject() gained argument 'format' in order to support
+ also RDS files (in addition to XDR files). File formats XDR and RDS are
+ supported. The default format is inferred from the filename extension. If
+ this is not possible, then the XDR format is assumed (default; backward
+ compatible).
+
+ o mkdirs() gained arguments 'mustWork' and 'maxTries'.
+
+ o seqToHumanReadable() gained argument 'tau'.
+
+ o R.utils::commandArgs() now also ackowledges 'argv' set by the littler
+ executable.
+
+ o R.utils::commandArgs() recognizes more reserved command-line arguments, e.g.
+ --debugger-args=N, --min-vsize=N and --min-nsize=N.
+
+ o ROBUSTNESS: Now writeDataFrame(..., sep, quote = FALSE) asserts that none of
+ the columns contains the field separator 'sep', because then the written
+ file would be corrupt/invalid.
+
+ o ROBUSTNESS: Explicit import of all 'graphics', 'grDevices', 'stats' and
+ 'utils' functions.
+
+DOCUMENTATION:
+
+ o Clarified in help for compressFile() et al. that these functions remove the
+ input file by default after the output file is generated. Thanks to Ben
+ Bond-Lamberty (Pacific Northwest National Laboratory) for pointing out this
+ potential pitfall.
+
+BUG FIXES:
+
+ o seqToHumanReadable(c(1:2, 4:5)) gave "1-2, 4, 5".
+
+ o withTimeout() did not work in non-English locales. Thanks to Arnaud Malapert
+ at University Nice Sophia Antipolis for reporting on this.
+
+ o GString ignored "simple" attributes, e.g. $[tolower]{y}. Thanks to Andre
+ Mikulec for reporting on this.
+
+ o downloadFile() via https://<user>:<pwd>@<domain>/ gave an error.
+
+DEPRECATE AND DEFUNCT:
+ o CLEANUP: Deprecated resetWarnings().
+
+
Version: 2.1.0 [2015-05-27]
-o Added compressPDF() to compress PDFs.
-o If, and only if, 'path' is an existing directory, then
- copyFile(pathname, path) copies file 'pathname' to the 'path'
- directory (previously destination always had to be a file).
- Analogously, renameFile(pathname, path) moves file 'pathname'
- (not a directory though) to destination directory 'path'.
-o CLEANUP: createLink(..., skip=TRUE) would give a false warning
- if a proper link already existed and the target was elsewhere
- than the current directory.
-o INCONSISTENCY: captureOutput(..., collapse="\n") did not drop
- newline of the last line as captureOutput(..., collapse="\r")
- and any other collapse != "\n" strings. Added package tests.
-o BUG FIX: captureOutput(..., file="foo.txt") gave an error.
+NEW FEATURES:
+ o Added compressPDF() to compress PDFs.
+
+ o If, and only if, 'path' is an existing directory, then copyFile(pathname,
+ path) copies file 'pathname' to the 'path' directory (previously destination
+ always had to be a file). Analogously, renameFile(pathname, path) moves file
+ 'pathname' (not a directory though) to destination directory 'path'.
+
+ o CLEANUP: createLink(..., skip = TRUE) would give a false warning if a proper
+ link already existed and the target was elsewhere than the current directory.
+
+ o INCONSISTENCY: captureOutput(..., collapse = "\n") did not drop newline of the
+ last line as captureOutput(..., collapse = "\r") and any other collapse != "\n"
+ strings. Added package tests.
+
+BUG FIXES:
+
+ o captureOutput(..., file = "foo.txt") gave an error.
+
+
Version: 2.0.2 [2015-04-27]
-o ROBUSTNESS: Now nchar(..., type="chars") is used internally for
- all file and directory names.
-o BUG FIX: Arguments$getReadablePathname(NA, mustExist=FALSE) no
- longer gives an error with recent R devel (>= 2015-04-23) related
- to an update on how nchar() handles missing values. This bug
- affected only Windows.
+BUG FIXES:
+
+ o Arguments$getReadablePathname(NA, mustExist = FALSE) no longer gives an error
+ with recent R devel (>= 2015-04-23) related to an update on how nchar()
+ handles missing values. This bug affected only Windows.
+CODE REFACTORING:
+
+ o ROBUSTNESS: Now nchar(..., type = "chars") is used internally for all file and
+ directory names.
+
+
Version: 2.0.1 [2015-04-24]
-o CLEANUP: R.utils no longer generates a warning if the R session
- is saved when R exits. Thanks to Jose Alquicira Hernandez for
- reporting on this.
-o BUG FIX: toCamelCase() with missing values would give an error
- in R devel (>= 2015-04-23) due to an update how nchar() handles
- missing values.
+NEW FEATURES:
+
+ o R.utils no longer generates a warning if the R session is saved when R
+ exits. Thanks to Jose Alquicira Hernandez for reporting on this.
+BUG FIXES:
+
+ o toCamelCase() with missing values would give an error in R devel
+ (>= 2015-04-23) due to an update how nchar() handles missing values.
+
+
Version: 2.0.0 [2015-02-28]
-o ROBUSTNESS: Package test coverage is 66%.
-o ROBUSTNESS: Now %<-% evaluates the expression in a local()
- environment, and it assign to environments, e.g. env$a %<-% 1.
-o R.utils::use() without arguments attaches 'R.utils'.
-o Added compressFile(), decompressFile() and isCompressedFile() methods,
- which gzip()/gunzip() and the new bzip2()/bunzip2() now use.
- Thanks to Peter Hickey for pushing for this.
-o Now eget() uses inherits=FALSE (was TRUE) and mode="default"
- (was "any"), where "default" corresponds to the mode of argument
- 'default', unless it's NULL when mode="any" is used.
-o Now commandArgs(asValues=TRUE, adhoc=TRUE) interprets 'x:=1:10'
- such that 'x' become the integer vector 1:10. Likewise, you can
- do 'x:=seq(1,3, by=0.1)' and 'x:=pi'. To get the string "pi",
- use quotation marks, i.e. 'x:="pi"', or just 'x=pi'.
-o Added cmsg(), cout(), ccat(), cprintf(), cprint(), cstr(), cshow()
- for outputting to "console", which is neither R stdout nor stderr
- and can therefor not be intercepted via capture.output(), sink()
- or similar. These functions are useful for outputting messages
- that requires user's attention and are often followed by a prompt
- via readline(), which also cannot be captured.
-o Added mpager() which is a "pager" function compatible with
- file.show() that will display file contents on standard error.
-o Just like for listDirectory(), argument 'recursive' of findFiles()
- can in addition to be FALSE (depth=0) and TRUE (depth=+Inf), be any
- non-negative numeric number specifying how deeply the recursive
- search should be done.
-o On Windows, Arguments$getReadablePathname() now gives an informative
- warning if a pathname of length 256 or longer is used/generated,
- which are not supported on Windows.
-o DOCUMENTATION: Fixed mistake in help("captureOutput").
- Thanks to Mikko Korpela (Issue #4) for reporting on this.
-o ROBUSTNESS: Forgot to declare "default" warnings() as an S3 method.
-o BUG FIX: use(..., quietly=FALSE) no longer captures/buffers the
- output, which prevented it from displaying full prompt messages
- that required a user response. use(..., quietly=TRUE), which is
- the default, no longer tries to ask user of Windows and OS X if
- they wish to install from source if the binary is older.
-o BUG FIX: Now the returned value of all withNnn() functions preserves
- the "visibility" of the eval():uated expression. Added package tests.
-o BUG FIX: withCapture({}) no longer generates a warning.
-o BUG FIX: Now isUrl(NA) returns FALSE (instead of NA).
-o BUG FIX: seqToIntervals(integer(0)) gave error "object 'res' not found".
-o BUG FIX: attachLocally() on an environment would remove the
- attached fields/variables from that environment.
+NEW FEATURES:
+
+ o ROBUSTNESS: Now %<-% evaluates the expression in a local() environment, and
+ it assign to environments, e.g. env$a %<-% 1.
+
+ o Added compressFile(), decompressFile() and isCompressedFile() methods, which
+ gzip()/gunzip() and the new bzip2()/bunzip2() now use. Thanks to Peter
+ Hickey for pushing for this.
+
+ o Now eget() uses inherits = FALSE (was TRUE) and mode = "default" (was
+ "any"), where "default" corresponds to the mode of argument 'default',
+ unless it's NULL when mode = "any" is used.
+
+ o Now commandArgs(asValues = TRUE, adhoc = TRUE) interprets 'x:=1:10' such that 'x'
+ become the integer vector 1:10. Likewise, you can do 'x:=seq(1,3, by = 0.1)'
+ and 'x:=pi'. To get the string "pi", use quotation marks, i.e. 'x:="pi"',
+ or just 'x=pi'.
+
+ o Added cmsg(), cout(), ccat(), cprintf(), cprint(), cstr(), cshow() for
+ outputting to "console", which is neither R stdout nor stderr and can
+ therefor not be intercepted via capture.output(), sink() or similar. These
+ functions are useful for outputting messages that requires user's attention
+ and are often followed by a prompt via readline(), which also cannot be
+ captured.
+
+ o Added mpager() which is a "pager" function compatible with file.show() that
+ will display file contents on standard error.
+
+ o Just like for listDirectory(), argument 'recursive' of findFiles() can in
+ addition to be FALSE (depth = 0) and TRUE (depth = +Inf), be any non-negative
+ numeric number specifying how deeply the recursive search should be done.
+
+ o On Windows, Arguments$getReadablePathname() now gives an informative warning
+ if a pathname of length 256 or longer is used/generated, which are not
+ supported on Windows.
+
+DOCUMENTATION:
+
+ o Fixed mistake in help("captureOutput"). Thanks to Mikko Korpela (Issue #4)
+ for reporting on this.
+
+BUG FIXES:
+
+ o use(..., quietly = FALSE) no longer captures/buffers the output, which
+ prevented it from displaying full prompt messages that required a user
+ response. use(..., quietly = TRUE), which is the default, no longer tries to
+ ask user of Windows and OS X if they wish to install from source if the
+ binary is older.
+
+ o Now the returned value of all withNnn() functions preserves the "visibility"
+ of the eval():uated expression. Added package tests.
+
+ o withCapture({}) no longer generates a warning.
+ o Now isUrl(NA) returns FALSE (instead of NA).
+
+ o seqToIntervals(integer(0)) gave error "object 'res' not found".
+
+ o attachLocally() on an environment would remove the attached fields/variables
+ from that environment.
+
+CODE REFACTORING:
+
+ o ROBUSTNESS: Forgot to declare "default" warnings() as an S3 method.
+
+ o R.utils::use() without arguments attaches 'R.utils'.
+
+ o ROBUSTNESS: Package test coverage is 66%.
+
+
+
Version: 1.34.0 [2014-10-07]
-o Added URL and BugReports fields to DESCRIPTION.
-o Submitted to CRAN.
+CODE REFACTORING:
+
+ o Added URL and BugReports fields to DESCRIPTION.
+ o Submitted to CRAN.
+
+
Version: 1.33.10 [2014-10-03]
-o Added shell.exec2(), which does a better job than shell.exec() in
- opening pathnames with forward slashes and files on mapped drives,
- which may or may not open depending software, e.g. Google Chrome
- fails to open the latter. Add options(browser=function(...)
- R.utils::shell.exec2(...)) to your ~/.Rprofile file to make
- browseURL() use this function instead of shell.exec(). This
- function is only useful on Windows.
-o BUG FIX: Now Arguments$getReadablePathname(file, path) ignores
- 'path' if 'file' specifies an absolute pathname.
+NEW FEATURES:
+ o Added shell.exec2(), which does a better job than shell.exec() in opening
+ pathnames with forward slashes and files on mapped drives, which may or may
+ not open depending software, e.g. Google Chrome fails to open the latter.
+ Add options(browser = function(...) R.utils::shell.exec2(...)) to your
+ ~/.Rprofile file to make browseURL() use this function instead of
+ shell.exec(). This function is only useful on Windows.
+
+BUG FIXES:
+
+ o Now Arguments$getReadablePathname(file, path) ignores 'path' if 'file'
+ specifies an absolute pathname.
+
+
Version: 1.33.9 [2014-10-03]
-o Now countLines() automatically supports gzipped files as well.
- Thanks to Sarah Nelson at Dept of Biostatistics at University
- of Washington for the suggestion.
-o Now downloadFile("https://...") will use 'curl', and if not available
- 'wget', to download the file over the HTTPS protocol. Previously
- only 'wget' was used. The 'curl' software is available on more
- operating systems, include OS X, whereas 'wget' sometimes needs
- a separate installation.
+NEW FEATURES:
+
+ o Now countLines() automatically supports gzipped files as well. Thanks to
+ Sarah Nelson at Dept of Biostatistics at University of Washington for the
+ suggestion.
+ o Now downloadFile("https://...") will use 'curl', and if not available 'wget',
+ to download the file over the HTTPS protocol. Previously only 'wget' was
+ used. The 'curl' software is available on more operating systems, include
+ OS X, whereas 'wget' sometimes needs a separate installation.
+
+
Version: 1.33.8 [2014-10-02]
-o Added argument 'unmap' to filePath() for "following" paths that are
- on mapped Windows drives.
-o CLEANUP: use() would try temporarily set package repository options
- even when not needed. This could trigger unnecessary warnings for
- users who haven't set a default CRAN mirror and using use() to
- load/attach an already installed package.
+NEW FEATURES:
+ o Added argument 'unmap' to filePath() for "following" paths that are on
+ mapped Windows drives.
+
+ o CLEANUP: use() would try temporarily set package repository options even
+ when not needed. This could trigger unnecessary warnings for users who
+ haven't set a default CRAN mirror and using use() to load/attach an already
+ installed package.
+
+
Version: 1.33.7 [2014-09-18]
-o New default for writeDataFrame() - argument 'col.names=!append'.
- Also, if append=TRUE, header comments are only written if specified.
- Added package system test for writeDataFrame().
+NEW FEATURES:
+ o New default for writeDataFrame() - argument 'col.names = !append'. Also, if
+ append = TRUE, header comments are only written if specified. Added package
+ system test for writeDataFrame().
+
+
Version: 1.33.6 [2014-09-16]
-o BUG FIX: getAbsolutePath("/tmp", expandTilde=TRUE) returned "//tmp".
- This would in turn have implications on getRelativePath(), e.g.
- getRelativePath("/tmp/a", relativeTo="/tmp") returned "../../tmp/a".
+BUG FIXES:
+ o getAbsolutePath("/tmp", expandTilde = TRUE) returned "//tmp". This would in
+ turn have implications on getRelativePath(), e.g. getRelativePath("/tmp/a",
+ relativeTo = "/tmp") returned "../../tmp/a".
+
+
Version: 1.33.5 [2014-09-15]
-o Added withSeed() and withSink().
-o ROBUSTNESS: Now withOptions() also resets all the options available
- upon entry even if no explicit options were specified. This covers
- the case when 'expr' changes the options and/or adds new options, e.g.
- withOptions({ options(width=10, foo="new"); str(letter) }).
+NEW FEATURES:
+
+ o Added withSeed() and withSink().
+ o ROBUSTNESS: Now withOptions() also resets all the options available upon
+ entry even if no explicit options were specified. This covers the case when
+ 'expr' changes the options and/or adds new options, e.g.
+ withOptions({ options(width = 10, foo = "new"); str(letter) }).
+
+
Version: 1.33.4 [2014-09-05]
-o ROBUSTNESS: Arguments$getWritablePathname() could sometimes generate
- warning "file.remove(pathnameT) : cannot remove file 'file...',
- reason 'Permission denied'. Now it tries to remove that files
- several times before giving up.
+BUG FIXES:
+ o ROBUSTNESS: Arguments$getWritablePathname() could sometimes generate warning
+ "file.remove(pathnameT) : cannot remove file 'file...', reason 'Permission
+ denied'. Now it tries to remove that files several times before giving up.
+
+
Version: 1.33.3 [2014-09-04]
-o ROBUSTNESS: Now copyDirectory(), just as copyFile() already did,
- silently drops arguments 'copy.mode' and 'copy.date' for older
- R versions where base::file.copy() does not support them.
+NEW FEATURES:
+ o ROBUSTNESS: Now copyDirectory(), just as copyFile() already did, silently
+ drops arguments 'copy.mode' and 'copy.date' for older R versions where
+ base::file.copy() does not support them.
+
+
Version: 1.33.2 [2014-09-01]
-o BUG FIX: mkdirs() could return "object 'res' not found" error.
+BUG FIXES:
+ o mkdirs() could return "object 'res' not found" error.
+
+
Version: 1.33.1 [2014-08-25]
-o BUG FIX: countLines() would not count the last line if it did
- not contain a newline. It would also give an error if the newline
- characters were only CR. This despite it was documented that both
- cases were supported. Added package system tests for them.
+BUG FIXES:
+ o countLines() would not count the last line if it did not contain a newline.
+ It would also give an error if the newline characters were only CR. This
+ despite it was documented that both cases were supported. Added package
+ system tests for them.
+
+
Version: 1.33.0 [2014-08-24]
-o Added mprint(), mcat(), mstr(), mshow() and mprintf() that work like
- the corresponding print(), cat(), etc., but output using message(),
- which in turn sends to standard error (instead of standard output).
- See also mout().
-o Added withLocale().
-o Now the test for target discrepancies by createLink(..., skip=TRUE)
- is more forgiving on Windows (by assuming a case-insensitive file
- system) before generating a warning.
-o Now useRepos(..., fallback=TRUE), and hence use(), will fallback to
- known/predefined CRAN repositories in case '@CRAN@' is not set.
- If done, it will give an informative warning message.
-o BUG FIX: commandArgs() would drop command-line arguments with periods,
- hyphens, or underscores in their names, e.g. --src_file=x.
+NEW FEATURES:
-Version: 1.32.6 [2014-08-12]
-o BUG FIX: withCapture({ if (T) 1 else 2 }) would give a parse error on
- "unexpected 'else'", because the internal deparsing puts the 'else'
- statement on a new line whenever an if-else statement is enclosed
- in an { ... } expression. This problem is also described in R help
- thread "deparse() and the 'else' statement" by Yihui Xie on 2009-11-09
- [http://tolstoy.newcastle.edu.au/R/e8/help/09/11/4204.html]. The
- workaround is to detect standalone 'else' statements and merge them
- with the previous line. Added package system test for this case.
+ o Added mprint(), mcat(), mstr(), mshow() and mprintf() that work like the
+ corresponding print(), cat(), etc., but output using message(), which in
+ turn sends to standard error (instead of standard output). See also mout().
+
+ o Added withLocale().
+
+ o Now the test for target discrepancies by createLink(..., skip = TRUE) is
+ more forgiving on Windows (by assuming a case-insensitive file system)
+ before generating a warning.
+
+ o Now useRepos(..., fallback = TRUE), and hence use(), will fallback to
+ known/predefined CRAN repositories in case '@CRAN@' is not set. If done, it
+ will give an informative warning message.
+BUG FIXES:
+ o commandArgs() would drop command-line arguments with periods, hyphens, or
+ underscores in their names, e.g. --src_file=x.
+
+
+Version: 1.32.6 [2014-08-12]
+
+BUG FIXES:
+
+ o withCapture({ if (T) 1 else 2 }) would give a parse error on "unexpected
+ 'else'", because the internal deparsing puts the 'else' statement on a new
+ line whenever an if-else statement is enclosed in an { ... } expression.
+ This problem is also described in R help thread "deparse() and the 'else'
+ statement" by Yihui Xie on 2009-11-09
+ [http://tolstoy.newcastle.edu.au/R/e8/help/09/11/4204.html]. The workaround
+ is to detect standalone 'else' statements and merge them with the previous
+ line. Added package system test for this case.
+
+
Version: 1.32.5 [2014-05-15]
-o BUG FIX: egsub() would return an invalid expression if the input had
- definitions of functions without arguments, e.g.
- egsub("x", "x", substitute(y <- function() 0)) which would throw
- "Error: badly formed function expression" if deparsed/printed.
- Added package test for this.
+BUG FIXES:
+ o egsub() would return an invalid expression if the input had definitions of
+ functions without arguments, e.g. egsub("x", "x", substitute(y <-
+ function() 0)) which would throw "Error: badly formed function expression"
+ if deparsed/printed. Added package test for this.
+
+
Version: 1.32.4 [2014-05-14]
-o Now egsub() also works with functions, in case it substitutes on
- the body of the function.
-o DOCUMENTATION: Added clarification to help("withTimeout") on the
- limitations of the function and when it is/is not possible to
- interrupt a function via timeouts.
-o Made the package test on absolute and relative paths less conservative,
- because it gave an error on Windows systems that have set R_USER to a
- Cygwin-flavored directory, which causes normalizePath("~") to return a
- non-existing directory. Thanks Uwe Ligges (CRAN) for reporting on this.
+NEW FEATURES:
+
+ o Now egsub() also works with functions, in case it substitutes on the body of
+ the function.
+
+DOCUMENTATION:
+
+ o Added clarification to help("withTimeout") on the limitations of the
+ function and when it is/is not possible to interrupt a function via timeouts.
+SOFTWARE QUALITY:
+
+ o Made the package test on absolute and relative paths less conservative,
+ because it gave an error on Windows systems that have set R_USER to a
+ Cygwin-flavored directory, which causes normalizePath("~") to return a
+ non-existing directory. Thanks Uwe Ligges (CRAN) for reporting on this.
+
+
Version: 1.32.3 [2014-05-08]
-o filePath("./././././") now returns "." (was ""). Added package
- system tests for filePath().
+BUG FIXES:
+ o filePath("./././././") now returns "." (was ""). Added package system tests
+ for filePath().
+
+
Version: 1.32.2 [2014-05-07]
-o Added support for substitution of expressions in withCapture()
- based on regular expressions utilizing new egsub().
-o Added egsub(), which is gsub() for expressions with some bells
- and whistles.
+NEW FEATURES:
+
+ o Added support for substitution of expressions in withCapture() based on
+ regular expressions utilizing new egsub().
+ o Added egsub(), which is gsub() for expressions with some bells and whistles.
+
+
Version: 1.32.1 [2014-05-04]
-o Now downloadFile() "adjusts" the output filename by decoding URL
- encoded characters, e.g. 'Hello%20world.txt' becomes 'Hello world.txt'.
- Also, unsafe filename characters (':', '*', '\') are encoded, e.g.
- 'How_to:_RSP.txt' becomes 'How_to%3A_RSP.txt'.
-o Added argument 'adjust' to Arguments$getReadablePathname(). When
- adjust="url" it decodes and encodes the filename the same way as
- downloadFile() now adjusts it (see above).
+NEW FEATURES:
+
+ o Now downloadFile() "adjusts" the output filename by decoding URL encoded
+ characters, e.g. 'Hello%20world.txt' becomes 'Hello world.txt'. Also,
+ unsafe filename characters (':', '*', '\') are encoded, e.g.
+ 'How_to:_RSP.txt' becomes 'How_to%3A_RSP.txt'.
+ o Added argument 'adjust' to Arguments$getReadablePathname(). When adjust =
+ "url" it decodes and encodes the filename the same way as downloadFile()
+ now adjusts it (see above).
+
+
Version: 1.32.0 [2014-05-01]
-o Added captureOutput() which is much faster than capture.output()
- for large outputs. withCapture() utilizes this now. Added package
- system tests for both functions.
-o use() now installs missing packages from all set repositories (as before)
- and uses the mainstream (CRAN and BioC) ones as fall backs.
-o Added withRepos() for installing/updating packages using a set of
- temporarily set repositories. It is possible to specify repositories
- by names, which are then selected from a set of known repositories,
- e.g. withRepos(install.packages("edgeR"), repos="[[BioC]]").
-o Added withOptions() for evaluating an expression with a set of
- options temporarily set.
-o Renamed evalCapture() to withCapture() and evalWithTimeout() and
- withTimeout(). The old name is kept for backward compatibility,
- but will eventually be deprecated.
+NEW FEATURES:
+
+ o Added captureOutput() which is much faster than capture.output() for large
+ outputs. withCapture() utilizes this now. Added package system tests for
+ both functions.
+
+ o use() now installs missing packages from all set repositories (as before)
+ and uses the mainstream (CRAN and BioC) ones as fall backs.
+
+ o Added withRepos() for installing/updating packages using a set of
+ temporarily set repositories. It is possible to specify repositories by
+ names, which are then selected from a set of known repositories, e.g.
+ withRepos(install.packages("edgeR"), repos = "[[BioC]]").
+ o Added withOptions() for evaluating an expression with a set of options
+ temporarily set.
+
+ o Renamed evalCapture() to withCapture() and evalWithTimeout() and
+ withTimeout(). The old name is kept for backward compatibility, but will
+ eventually be deprecated.
+
+
Version: 1.31.1 [2014-04-29]
-o ROBUSTNESS: Now use("<repos>::<pkg>") will detect when a repository
- is unknown and give an informative error message on how to update
- option 'repos'.
+NEW FEATURES:
+ o Now use("<repos>::<pkg>") will detect when a repository is unknown and give
+ an informative error message on how to update option 'repos'.
+
+
Version: 1.31.0 [2014-04-26]
-o Added assignment operator %<-% for delayed assignments.
-o Added option "evalCapture/newline".
+NEW FEATURES:
+
+ o Added assignment operator %<-% for delayed assignments.
+ o Added option "evalCapture/newline".
+
+
Version: 1.30.7 [2014-04-26]
-o Added argument 'xtrim' to draw() for density object.
-o CLEANUP: createLink(..., skip=TRUE) no longer warns if the link file
- was skipped. Now it only warns if the skipped link file links to a
- different file than the intended target file.
-o CLEANUP: Dropping '::' in calls where possible.
+NEW FEATURES:
+
+ o Added argument 'xtrim' to draw() for density object.
+ o CLEANUP: createLink(..., skip = TRUE) no longer warns if the link file was
+ skipped. Now it only warns if the skipped link file links to a different
+ file than the intended target file.
+
+CODE REFACTORING:
+
+ o CLEANUP: Dropping '::' in calls where possible.
+
+
Version: 1.30.6 [2014-04-24]
-o Added argument 'newline' to evalCapture().
+NEW FEATURES:
+ o Added argument 'newline' to evalCapture().
+
+
Version: 1.30.5 [2014-04-22]
-o Added argument 'substitute' to evalCapture() for substituting
- symbols "on the fly" in the expression before it is evaluated.
+NEW FEATURES:
+ o Added argument 'substitute' to evalCapture() for substituting symbols "on
+ the fly" in the expression before it is evaluated.
+
+
Version: 1.30.4 [2014-04-18]
-o Added argument 'modifiedOnly' to sourceDirectory(), which was
- previously passed via '...' to sourceTo(), and it now defaults
- to TRUE.
+NEW FEATURES:
+ o Added argument 'modifiedOnly' to sourceDirectory(), which was previously
+ passed via '...' to sourceTo(), and it now defaults to TRUE.
+
+
Version: 1.30.3 [2014-04-15]
-o BUG FIX: use() would not install package dependencies.
+BUG FIXES:
+ o use() would not install package dependencies.
+
+
Version: 1.30.2 [2014-04-08]
-o Added argument 'max.deparse.length' to evalCapture().
+NEW FEATURES:
+ o Added argument 'max.deparse.length' to evalCapture().
+
+
Version: 1.30.1 [2014-04-06]
-o Now evalCapture() utilizes deparse() to get the source code and
- acknowledges options 'deparse.cutoff' to control the code wrapping.
- Previously capture.output(print()) was used.
-o WORKAROUND: moveInSearchPath() redirects any messages to stderr that
- base::attach() sent to stdout. UPDATE: This attach() issue has been
- fixed in R 3.1.0 patched.
+NEW FEATURES:
+
+ o Now evalCapture() utilizes deparse() to get the source code and acknowledges
+ options 'deparse.cutoff' to control the code wrapping. Previously
+ capture.output(print()) was used.
+BUG FIXES:
+
+ o WORKAROUND: moveInSearchPath() redirects any messages to stderr that
+ base::attach() sent to stdout. UPDATE: This attach() issue has been fixed
+ in R 3.1.0 patched.
+
+
Version: 1.30.0 [2014-04-06]
-o Vectorized detachPackage(), getAbsolutePath(), getRelativePath(),
- isAbsolutePath(), isDirectory(), isFile(), isOpen(),
- isPackageInstalled(), touchFile() and toUrl(). Added package system
- tests for several of them. For backward compatibility,
- getAbsolutePath(), getRelativePath(), isAbsolutePath(), isFile() and
- isDirectory() treats an empty vector of path/pathnames equal to ".".
- However, in a future version, empty results will returned by these too.
-o BUG FIX: toCamelCase(character(0L)) gave an error.
+NEW FEATURES:
+
+ o Vectorized detachPackage(), getAbsolutePath(), getRelativePath(),
+ isAbsolutePath(), isDirectory(), isFile(), isOpen(), isPackageInstalled(),
+ touchFile() and toUrl(). Added package system tests for several of them.
+ For backward compatibility, getAbsolutePath(), getRelativePath(),
+ isAbsolutePath(), isFile(), and isDirectory() treats an empty vector of
+ path/pathnames equal to ".". However, in a future version, empty results
+ will returned by these too.
+
+BUG FIXES:
+ o toCamelCase(character(0L)) gave an error.
+
+
Version: 1.29.11 [2014-04-02]
-o BUG FIX: str() and summary() for Verbose did not acknowledge
- argument 'level'.
+BUG FIXES:
+ o str() and summary() for Verbose did not acknowledge argument 'level'.
+
+
Version: 1.29.10 [2014-02-28]
-o DOCUMENTATION: Added a help section on privileges required on Windows
- in order for createLink() to work.
+DOCUMENTATION:
+ o Added a help section on privileges required on Windows in order for
+ createLink() to work.
+
+
Version: 1.29.9 [2014-02-24]
-o ROBUSTNESS: Added a package redundancy test for a bug occurring in
- R.oo (< 1.18.0) causing R to core dump (with "Error: SET_VECTOR_ELT()
- can only be applied to a 'list', not a 'integer'") or gives an error
- (with "Error: not a weak reference") under certain conditions when a
- registered finalizer tried to reload R.oo if it was unloaded. This
- occurred only on R prior to R 3.0.2 patched (2014-02-21 r65057). Also,
- the 'methods' package needs to be attached, so it is still not clear
- what is the true cause of the bug. In R.oo (>= 1.18.0) this bug is
- avoided.
-
+NEW FEATURES:
+
+ o ROBUSTNESS: Added a package redundancy test for a bug occurring in R.oo
+ (< 1.18.0) causing R to core dump (with "Error: SET_VECTOR_ELT() can only be
+ applied to a 'list', not a 'integer'") or gives an error (with "Error: not a
+ weak reference") under certain conditions when a registered finalizer tried
+ to reload R.oo if it was unloaded. This occurred only on R prior to R 3.0.2
+ patched (2014-02-21 r65057). Also, the 'methods' package needs to be
+ attached, so it is still not clear what is the true cause of the bug. In
+ R.oo (>= 1.18.0) this bug is avoided.
+
+
Version: 1.29.8 [2014-01-27]
-o BUG FIX: Although eget(K=2, cmdArgs=TRUE) would use command-line
- argument 'K=1' as the default (instead of K=2), calling
- eget("K", 2, cmdArgs=TRUE) would not.
-o BUG FIX: commandArgs(excludeReserved=TRUE) failed to drop reserved
- arguments of type --<key>=<value>, e.g. --encoding=ASCII.
+BUG FIXES:
+
+ o Although eget(K = 2, cmdArgs = TRUE) would use command-line argument 'K=1'
+ as the default (instead of K=2), calling eget("K", 2, cmdArgs = TRUE) would
+ not.
+ o commandArgs(excludeReserved = TRUE) failed to drop reserved arguments of
+ type --<key>=<value>, e.g. --encoding=ASCII.
+
+
Version: 1.29.7 [2014-01-27]
-o Added trial version of the CmdArgsFunction class.
+NEW FEATURES:
+ o Added trial version of the CmdArgsFunction class.
+
+
Version: 1.29.6 [2014-01-27]
-o Added cmdArgsCall() for easy calling of functions from the command
- line, e.g. Rscript -e R.utils::cmdArgsCall(rnorm) n=4.
+NEW FEATURES:
+ o Added cmdArgsCall() for easy calling of functions from the command line,
+ e.g. Rscript -e R.utils::cmdArgsCall(rnorm) n=4.
+
+
Version: 1.29.5 [2014-01-27]
-o doCall() gained argument 'envir', which also means that the new
- behavior is to evaluate the call within the calling frame. Also,
- doCall() now accepts call a function object in addition to a name
- of a function.
+NEW FEATURES:
+ o doCall() gained argument 'envir', which also means that the new behavior is
+ to evaluate the call within the calling frame. Also, doCall() now accepts
+ call a function object in addition to a name of a function.
+
+
Version: 1.29.4 [2014-01-26]
-o Added argument 'unique' to cmdArgs().
-o Now commandArgs(asValues=TRUE) returns no-named arguments as a
- list element with the argument as the value and with a "" name.
- For instance, in the past one would get list(R=NA, a="1", noname=NA)
- whereas now one gets list("R", a="1", "noname").
-o BUG FIX: Now attachLocally() no longer tries to attach elements with
- an empty name, e.g. list(a=1, 2). Previously it gave an error.
- Added a package system test for attachLocally().
+NEW FEATURES:
+
+ o Added argument 'unique' to cmdArgs().
+ o Now commandArgs(asValues = TRUE) returns no-named arguments as a list
+ element with the argument as the value and with a "" name. For instance, in
+ the past one would get list(R = NA, a = "1", noname = NA) whereas now one
+ gets list("R", a = "1", "noname").
+
+BUG FIXES:
+
+ o Now attachLocally() no longer tries to attach elements with an empty name,
+ e.g. list(a = 1, 2). Previously it gave an error. Added a package system
+ test for attachLocally().
+
+
Version: 1.29.3 [2014-01-19]
-o CONSISTENCY: Now createLink(..., method="windows-shortcut") returns
- the path/pathname to the link (and not the target) just like it does
- for the other types of file links. By link we here mean the
- path/pathname without the *.lnk extension.
-o ROBUSTNESS: Added package system tests for createLink().
+NEW FEATURES:
+
+ o CONSISTENCY: Now createLink(..., method = "windows-shortcut") returns the
+ path/pathname to the link (and not the target) just like it does for the
+ other types of file links. By link we here mean the path/pathname without
+ the *.lnk extension.
+SOFTWARE QUALITY:
+
+ o ROBUSTNESS: Added package system tests for createLink().
+
+
Version: 1.29.2 [2014-01-12]
-o Now Arguments$getCharacters() preserves attributes. Also, made
- argument 'useNames' defaults to TRUE.
-o Added [() for GenericSummary.
+NEW FEATURES:
+
+ o Now Arguments$getCharacters() preserves attributes. Also, made argument
+ 'useNames' defaults to TRUE.
+ o Added [() for GenericSummary.
+
+
Version: 1.29.1 [2014-01-10]
-o Added argument 'what' to Sys.readlink2(), where what="corrected"
- makes sure to return the proper target path (not just the one
- relative to where the link lives).
+NEW FEATURES:
+ o Added argument 'what' to Sys.readlink2(), where what = "corrected" makes
+ sure to return the proper target path (not just the one relative to where
+ the link lives).
+
+
Version: 1.29.0 [2014-01-07]
-o The following file I/O methods follows symbolic links (also on Windows)
- and returns information based on the target file/directory (rather than
- the link itself): fileAccess(), file.info2(), isDirectory(), isFile()
- and lastModified().
-o Added file.info2() for retrieving file information such that symbolic
- file links are also acknowledged on Windows.
-o Added Sys.readlink2() for reading symbolic file links also on Windows.
-o removeDirectory() can now be used to remove symbolic directory links
- (also on Windows where neither file.remove() nor unlink() work).
- The target directory will never be removed.
-o BUG FIX: renameFile() would give an error on directories.
-o Added package system tests for copyFile() and renameFile().
-o ROBUSTNESS: createLink() will no longer try to create Windows file
- links on non-Windows platforms.
-o ROBUSTNESS: Updated a shell() calls that assume the Windows command
- interpreter to explicitly specify shell=Sys.getenv("COMSPEC").
+ o The following file I/O methods follows symbolic links (also on Windows)
+ and returns information based on the target file/directory (rather than
+ the link itself): fileAccess(), file.info2(), isDirectory(), isFile()
+ and lastModified().
-Version: 1.28.6 [2014-01-06]
-o Added argument 'skip' (in addition to existing 'overwrite') to copyFile()
- to allow for better control on how to handle existing destination files.
- For backward compatibilities, it defaults to FALSE, but may be changed
- to skip=!overwrite in a future version. Furthermore, copyFile() now
- passes (known) arguments '...' to base::file.copy() making it possible
- to copy with or without file permissions etc. Thanks Taku Tokuyasu (UCSF)
- for reporting on this.
+ o Added file.info2() for retrieving file information such that symbolic
+ file links are also acknowledged on Windows.
+ o Added Sys.readlink2() for reading symbolic file links also on Windows.
+ o removeDirectory() can now be used to remove symbolic directory links
+ (also on Windows where neither file.remove() nor unlink() work).
+ The target directory will never be removed.
+
+ o BUG FIX: renameFile() would give an error on directories.
+
+ o Added package system tests for copyFile() and renameFile().
+
+ o ROBUSTNESS: createLink() will no longer try to create Windows file
+ links on non-Windows platforms.
+
+ o ROBUSTNESS: Updated a shell() calls that assume the Windows command
+ interpreter to explicitly specify shell = Sys.getenv("COMSPEC").
+
+
+Version: 1.28.6 [2014-01-06]
+
+ o Added argument 'skip' (in addition to existing 'overwrite') to copyFile()
+ to allow for better control on how to handle existing destination files.
+ For backward compatibilities, it defaults to FALSE, but may be changed
+ to skip = !overwrite in a future version. Furthermore, copyFile() now
+ passes (known) arguments '...' to base::file.copy() making it possible
+ to copy with or without file permissions etc. Thanks Taku Tokuyasu (UCSF)
+ for reporting on this.
+
+
Version: 1.28.5 [2013-12-15]
-o Now argument 'asGString' for Arguments$getCharacters() defaults to
- getOption("Arguments$getCharacters/args/asGString", TRUE). This makes
- it possible to disable this feature, even when it is not possible to
- directly pass that argument. This will also make it possible to
- set the default to FALSE in the future (instead of TRUE as today).
-o Added argument 'inherits' to evaluate() for GString. Default
- is TRUE for backward compatibility.
+ o Now argument 'asGString' for Arguments$getCharacters() defaults to
+ getOption("Arguments$getCharacters/args/asGString", TRUE). This makes
+ it possible to disable this feature, even when it is not possible to
+ directly pass that argument. This will also make it possible to
+ set the default to FALSE in the future (instead of TRUE as today).
+ o Added argument 'inherits' to evaluate() for GString. Default
+ is TRUE for backward compatibility.
+
+
Version: 1.28.4 [2013-11-20]
-o Minor updates to NAMESPACE file.
-
+ o Minor updates to NAMESPACE file.
+
+
Version: 1.28.3 [2013-11-15]
-o Added method c() for GenericSummary.
-
+ o Added method c() for GenericSummary.
+
+
Version: 1.28.2 [2013-11-15]
-o CLEANUP: Arguments$getNumerics(NA, range=c(0,1)) no longer gives
- warnings on "no non-missing arguments to min()" etc.
-
+ o CLEANUP: Arguments$getNumerics(NA, range = c(0,1)) no longer gives
+ warnings on "no non-missing arguments to min()" etc.
+
+
Version: 1.28.1 [2013-10-30]
-o BUG FIX: System$getMappedDrivesOnWindows() failed to return the
- proper path for 'net use' mounted drives, iff the path contained
- spaces.
-
+ o BUG FIX: System$getMappedDrivesOnWindows() failed to return the
+ proper path for 'net use' mounted drives, iff the path contained
+ spaces.
+
+
Version: 1.28.0 [2013-10-20]
-o CLEANUP: Removed a few non-used internal objects.
-o Forgot to declare enterf() for Verbose as an S3 method.
+ o CLEANUP: Removed a few non-used internal objects.
+ o Forgot to declare enterf() for Verbose as an S3 method.
+
+
Version: 1.27.6 [2013-10-13]
-o CLEANUP: Some methods had to attach 'R.utils' in the past in order
- to work properly. These are no longer attaching 'R.utils':
- copyDirectory(), createLink(), createWindowsShortcut(), downloadFile(),
- installPackages(), removeDirectory(), and sourceDirectory().
-o Bumped up package dependencies.
+ o CLEANUP: Some methods had to attach 'R.utils' in the past in order
+ to work properly. These are no longer attaching 'R.utils':
+ copyDirectory(), createLink(), createWindowsShortcut(), downloadFile(),
+ installPackages(), removeDirectory(), and sourceDirectory().
+ o Bumped up package dependencies.
+
+
Version: 1.27.5 [2013-10-07]
-o CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
-o CLEANUP: Dropped obsolete autoload():s.
-o ROBUSTNESS: The overriding of getOption() to become a generic
- function does now call base::getOption() in the default, instead
- of copy the latter.
-o Bumped up package dependencies.
+ o CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
+
+ o CLEANUP: Dropped obsolete autoload():s.
+
+ o ROBUSTNESS: The overriding of getOption() to become a generic
+ function does now call base::getOption() in the default, instead
+ of copy the latter.
+ o Bumped up package dependencies.
+
+
Version: 1.27.4 [2013-09-28]
-o Now argument 'recursive' of listDirectory() can also specify the
- maximum recursive depth, e.g listDirectory(..., recursive=5L).
-o Now the 'R.utils' Package object is also available when the
- package is only loaded (but not attached).
+ o Now argument 'recursive' of listDirectory() can also specify the
+ maximum recursive depth, e.g listDirectory(..., recursive = 5L).
+ o Now the 'R.utils' Package object is also available when the
+ package is only loaded (but not attached).
+
+
Version: 1.27.3 [2013-09-20]
-o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().
-
+ o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().
+
+
Version: 1.27.2 [2013-09-15]
-o TYPO: An error message of dimNA<-() was referring to 'files'
- rather than to 'elements'.
-
+ o TYPO: An error message of dimNA<-() was referring to 'files'
+ rather than to 'elements'.
+
+
Version: 1.27.1 [2013-09-10]
-o BUG FIX: commandArgs(asValues=TRUE) failed to set the value of
- the very last argument to TRUE if it was a flag, e.g.
- 'R --args --bar'. Thanks to Stijn van Dongen at EMBL-EBI in
- Cambridge/Hinxton, UK for reporting on this.
-
+ o BUG FIX: commandArgs(asValues = TRUE) failed to set the value of
+ the very last argument to TRUE if it was a flag, e.g.
+ 'R --args --bar'. Thanks to Stijn van Dongen at EMBL-EBI in
+ Cambridge/Hinxton, UK for reporting on this.
+
+
Version: 1.27.0 [2013-08-30]
-o Added use() for easy attaching/loading and automatic installation
- of packages.
-o Now isPackageInstalled() suppresses warnings.
+ o Added use() for easy attaching/loading and automatic installation
+ of packages.
+ o Now isPackageInstalled() suppresses warnings.
+
+
Version: 1.26.4 [2013-08-27]
-o CLEANUP: Arguments$getReadablePathnames(files, paths=NULL) no longer
- warns about "rep(paths, length.out = nbrOfFiles) : 'x' is NULL so
- the result will be NULL" if length(files) > 0.
-o CLEANUP: Package no longer utilizes ':::'.
-o DOCUMENTATION: Help for installPackages() was missing. Thanks
- Gabor Grothendieck for reporting on this.
+ o CLEANUP: Arguments$getReadablePathnames(files, paths = NULL) no longer
+ warns about "rep(paths, length.out = nbrOfFiles) : 'x' is NULL so
+ the result will be NULL" if length(files) > 0.
-Version: 1.26.3 [2013-08-20]
-o Forgot to declare default inherits() as an S3 method.
+ o CLEANUP: Package no longer utilizes ':::'.
+ o DOCUMENTATION: Help for installPackages() was missing. Thanks
+ Gabor Grothendieck for reporting on this.
+
+
+Version: 1.26.3 [2013-08-20]
+ o Forgot to declare default inherits() as an S3 method.
+
+
Version: 1.26.2 [2013-07-30]
-o ROBUSTNESS/BUG FIX: System$findGhostscript() could still
- give errors. Completely rewrote how Ghostscripts is searched.
- On Windows, environment variable 'GSC' is now also searched.
- Thanks to Brian Ripley for the feedback.
-
+ o ROBUSTNESS/BUG FIX: System$findGhostscript() could still
+ give errors. Completely rewrote how Ghostscripts is searched.
+ On Windows, environment variable 'GSC' is now also searched.
+ Thanks to Brian Ripley for the feedback.
+
+
Version: 1.26.1 [2013-07-29]
-o BUG FIX: System$findGhostscript() would give "Error in pathname
- [sapply(pathname, FUN = isFile)]: invalid subscript type 'list'"
- if no device was found.
-
+ o BUG FIX: System$findGhostscript() would give "Error in pathname
+ [sapply(pathname, FUN = isFile)]: invalid subscript type 'list'"
+ if no device was found.
+
+
Version: 1.26.0 [2013-07-27]
-o Added tempvar() for creating non-existing temporary variables.
-o Added enterf() to Verbose, which is an sprintf-like enter().
-o Now System$findGhostscript() returns system variable 'R_GSCMD' if
- set and it refers to an existing executable (and unless force=TRUE).
- It then checks with Sys.which(). On Windows, it finally searches
- for 'gswin64c.exe' and 'gswin32c.exe' on known locations. Added
- arguments 'firstOnly' and 'force'.
-o Now getAbsolutePath() shortens paths if possible, e.g. "C:/foo/.."
- becomes "C:/".
-o Added argument 'skip' to gzip() and gunzip().
-o BUG FIX: gunzip() would ignore argument 'overwrite'.
-o BUG FIX: filePath("C:/foo/..") returned "C:", which should be "C:/".
+ o Added tempvar() for creating non-existing temporary variables.
-Version: 1.25.3 [2013-07-27]
-o BUG FIX: findSourceTraceback() would give an error "Unknown class of
- 'srcfile': character" for source(..., keep.source=FALSE) in recent
- R devel and R v3.0.1 patched. Thanks Duncan Murdoch for the report.
+ o Added enterf() to Verbose, which is an sprintf-like enter().
+
+ o Now System$findGhostscript() returns system variable 'R_GSCMD' if
+ set and it refers to an existing executable (and unless force = TRUE).
+ It then checks with Sys.which(). On Windows, it finally searches
+ for 'gswin64c.exe' and 'gswin32c.exe' on known locations. Added
+ arguments 'firstOnly' and 'force'.
+
+ o Now getAbsolutePath() shortens paths if possible, e.g. "C:/foo/.."
+ becomes "C:/".
+
+ o Added argument 'skip' to gzip() and gunzip().
+ o BUG FIX: gunzip() would ignore argument 'overwrite'.
+ o BUG FIX: filePath("C:/foo/..") returned "C:", which should be "C:/".
+
+
+Version: 1.25.3 [2013-07-27]
+
+ o BUG FIX: findSourceTraceback() would give an error "Unknown class of
+ 'srcfile': character" for source(..., keep.source = FALSE) in recent
+ R devel and R v3.0.1 patched. Thanks Duncan Murdoch for the report.
+
+
Version: 1.25.2 [2013-07-03]
-o Now installPackages() may also install from https URLs.
-o Now more methods can be used without attaching ("loading") the
- package: copyFile(), copyDirectory(), removeDirectory(), createLink(),
- createWindowsShortcut(), downloadFile(), sourceDirectory(), and
- installPackages(), e.g. R.utils::downloadFile().
-o Now touchFile() utilizes base::Sys.setFileTime(), iff available.
+ o Now installPackages() may also install from https URLs.
-Version: 1.25.1 [2013-07-01]
-o Bumped up package dependencies.
+ o Now more methods can be used without attaching ("loading") the
+ package: copyFile(), copyDirectory(), removeDirectory(), createLink(),
+ createWindowsShortcut(), downloadFile(), sourceDirectory(), and
+ installPackages(), e.g. R.utils::downloadFile().
+ o Now touchFile() utilizes base::Sys.setFileTime(), iff available.
+
+
+Version: 1.25.1 [2013-07-01]
+ o Bumped up package dependencies.
+
+
Version: 1.25.0 [2013-06-27]
-o UPDATE: Now gzip()/gunzip() returns the output file (was number
- of output bytes processed which are now returned as an attribute).
-o Added argument 'temporary' to gzip()/gunzip().
-o Added isGzipped() for testing whether a file is gzipped or not.
+ o UPDATE: Now gzip()/gunzip() returns the output file (was number
+ of output bytes processed which are now returned as an attribute).
-Version: 1.24.4 [2013-06-17]
-o Now argument 'dims' of extract() can also be dimension names.
+ o Added argument 'temporary' to gzip()/gunzip().
+ o Added isGzipped() for testing whether a file is gzipped or not.
+
+
+Version: 1.24.4 [2013-06-17]
+ o Now argument 'dims' of extract() can also be dimension names.
+
+
Version: 1.24.3 [2013-05-25]
-o Minor speedups by replacing rm() calls with NULL assignments.
-o SPEEDUP: readTable() no longer calls gc().
+ o Minor speedups by replacing rm() calls with NULL assignments.
+ o SPEEDUP: readTable() no longer calls gc().
+
+
Version: 1.24.2 [2013-05-20]
-o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
-o CRAN POLICY: Now all Rd example lines are at most 100 characters long.
+ o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
+ o CRAN POLICY: Now all Rd example lines are at most 100 characters long.
+
+
Version: 1.24.1 [2013-05-13]
-o The workaround needed by isDirectory() due to a bug in
- file.info() is now applied only for R (< 3.0.2), since the
- bug was been fixed in R 3.0.1 patched (PR#15302).
-
+ o The workaround needed by isDirectory() due to a bug in
+ file.info() is now applied only for R (< 3.0.2), since the
+ bug was been fixed in R 3.0.1 patched (PR#15302).
+
+
Version: 1.24.0 [2013-04-18]
-o Several methods now output messages and verbose output
- to standard error (instead of standard output), including
- addFinalizerToLast(), filePath(), patchCode(), readWindowsShellLink(),
- readWindowsShortcut(), and loadAnywhere() for Settings.
-
+ o Several methods now output messages and verbose output
+ to standard error (instead of standard output), including
+ addFinalizerToLast(), filePath(), patchCode(), readWindowsShellLink(),
+ readWindowsShortcut(), and loadAnywhere() for Settings.
+
+
Version: 1.23.4 [2013-04-15]
-o BUG FIX: capitalize()/decapitalize() would return "NANA" for
- missing values. Reported by Liviu Andronic.
-
+ o BUG FIX: capitalize()/decapitalize() would return "NANA" for
+ missing values. Reported by Liviu Andronic.
+
+
Version: 1.23.3 [2013-03-29]
-o BUG FIX: downloadFile('https://...') did not work if 'username'
- or 'password' was NULL.
-
+ o BUG FIX: downloadFile('https://...') did not work if 'username'
+ or 'password' was NULL.
+
+
Version: 1.23.2 [2013-03-22]
-o BUG FIX: Previous update caused commandArgs(..., adhoc=TRUE)
- to coerce 'T' and 'F' to logicals TRUE and FALSE. They are
- now preserved as character string.
-
+ o BUG FIX: Previous update caused commandArgs(..., adhoc = TRUE)
+ to coerce 'T' and 'F' to logicals TRUE and FALSE. They are
+ now preserved as character string.
+
+
Version: 1.23.1 [2013-03-21]
-o Now commandArgs(..., adhoc=TRUE) utilizes utils::type.convert().
-
+ o Now commandArgs(..., adhoc = TRUE) utilizes utils::type.convert().
+
+
Version: 1.23.0 [2013-03-20]
-o Added ecget() which is like eget() with the default value
- corresponding to the command-line argument.
-o Added eget() for retrieving a single variable, with a
- fallback to a default value, e.g. n <- eget(n=42).
-o Added support for cmdArg(n=42) as an alias to cmdArg("n", 42).
+ o Added ecget() which is like eget() with the default value
+ corresponding to the command-line argument.
-Version: 1.22.0 [2013-03-14]
-o Added cmdArg() for retrieving a single command line argument
- with a default value and type, e.g. n <- cmdArg("n", 42).
+ o Added eget() for retrieving a single variable, with a
+ fallback to a default value, e.g. n <- eget(n = 42).
+ o Added support for cmdArg(n = 42) as an alias to cmdArg("n", 42).
+
+
+Version: 1.22.0 [2013-03-14]
+ o Added cmdArg() for retrieving a single command line argument
+ with a default value and type, e.g. n <- cmdArg("n", 42).
+
+
Version: 1.21.2 [2013-03-11]
-o Bumped up package dependencies.
-
+ o Bumped up package dependencies.
+
+
Version: 1.21.1 [2013-03-08]
-o Added an Authors at R field to the DESCRIPTION.
-
+ o Added an Authors at R field to the DESCRIPTION.
+
+
Version: 1.21.0 [2013-03-07]
-o Major improvement of commandArgs(). For instance, now it never
- consider arguments after '--args' to be reserved or environment
- variable arguments; they are always user arguments. It is also
- doing a better job on interpreting -*<key>=<value> arguments;
- previously it could happen that it would split the <value>.
- Added systems test for commandArgs() and cmdArgs().
-
+ o Major improvement of commandArgs(). For instance, now it never
+ consider arguments after '--args' to be reserved or environment
+ variable arguments; they are always user arguments. It is also
+ doing a better job on interpreting -*<key>=<value> arguments;
+ previously it could happen that it would split the <value>.
+ Added systems test for commandArgs() and cmdArgs().
+
+
Version: 1.20.2 [2013-03-07]
-o Now argument 'eps' for isZero() may also be a character string
- specifying either "double.eps" or "single.eps".
-
+ o Now argument 'eps' for isZero() may also be a character string
+ specifying either "double.eps" or "single.eps".
+
+
Version: 1.20.1 [2013-03-04]
-o DOCUMENTATION: Updated the help usage section for all static methods.
-
+ o DOCUMENTATION: Updated the help usage section for all static methods.
+
+
Version: 1.20.0 [2013-02-24]
-o Added cmdArgs() which is short for R.utils::commandArgs(asValues=TRUE,
- adhoc=TRUE, unique=TRUE, excludeReserved=TRUE, ...)[-1L].
-o Now it is possible to specify default arguments in commandArgs().
- In addition, if asValues=TRUE, then the values of the parsed
- command-line arguments will be coerced to the data type of the
- default ones if they share names. If adhoc=TRUE, arguments will
- be coerced to numerics unless the result is NA.
-o For conveniency, getAbsolutePath() and getRelativePath() returns
- the same pathname if it is a URL.
-o Added gstring() and gcat().
-o Now it is possible to escape the sed-like search replace format
- for GString:s via quoting, e.g. ${'R.rsp/HttpDaemon/RspVersion'} .
-o BUG FIX: getParent() and filePath() as well as System$mapDriveOnWindows()
- and System$unmapDriveOnWindows() did not handle paths with a lower case
- Windows drive letter. Oddly, it is only now that we have received
- an single report (on a Windows 7 system) that such getwd() may return
- such drive letters, e.g. 'c:/path/' instead of 'C:/path/'.
-o BUG FIX: evaluate(..., where="parent") for GString would result
- in an endless loop.
-o BUG FIX: displayCode(code) incorrectly processed 'code' as GString:s.
+ o Added cmdArgs() which is short for R.utils::commandArgs(asValues = TRUE,
+ adhoc = TRUE, unique = TRUE, excludeReserved = TRUE, ...)[-1L].
-Version: 1.19.5 [2013-01-11]
-o BUG FIX: Specifying argument 'version' to isPackageLoaded() would give
- "Error: 'manglePackageName' is defunct." in recent versions of R.
- Thanks to Brian Ripley (R core) for reporting on this.
+ o Now it is possible to specify default arguments in commandArgs().
+ In addition, if asValues = TRUE, then the values of the parsed
+ command-line arguments will be coerced to the data type of the
+ default ones if they share names. If adhoc = TRUE, arguments will
+ be coerced to numerics unless the result is NA.
+
+ o For conveniency, getAbsolutePath() and getRelativePath() returns
+ the same pathname if it is a URL.
+
+ o Added gstring() and gcat().
+
+ o Now it is possible to escape the sed-like search replace format
+ for GString:s via quoting, e.g. ${'R.rsp/HttpDaemon/RspVersion'} .
+
+ o BUG FIX: getParent() and filePath() as well as System$mapDriveOnWindows()
+ and System$unmapDriveOnWindows() did not handle paths with a lower case
+ Windows drive letter. Oddly, it is only now that we have received
+ an single report (on a Windows 7 system) that such getwd() may return
+ such drive letters, e.g. 'c:/path/' instead of 'C:/path/'.
+ o BUG FIX: evaluate(..., where = "parent") for GString would result
+ in an endless loop.
+ o BUG FIX: displayCode(code) incorrectly processed 'code' as GString:s.
+
+
+Version: 1.19.5 [2013-01-11]
+
+ o BUG FIX: Specifying argument 'version' to isPackageLoaded() would give
+ "Error: 'manglePackageName' is defunct." in recent versions of R.
+ Thanks to Brian Ripley (R core) for reporting on this.
+
+
Version: 1.19.4 [2013-01-07]
-o Now '.Last.lib' is exported.
-o Bumped up package dependencies.
+ o Now '.Last.lib' is exported.
+ o Bumped up package dependencies.
+
+
Version: 1.19.3 [2012-12-19]
-o Utilizing new startupMessage() of R.oo.
-
+ o Utilizing new startupMessage() of R.oo.
+
+
Version: 1.19.2 [2012-12-18]
-o R CMD check for R devel no longer gives a NOTE on attach().
-
+ o R CMD check for R devel no longer gives a NOTE on attach().
+
+
Version: 1.19.1 [2012-12-02]
-o CLEANUP: R CMD check no longer warns on global assignments.
-o BUG FIX: Arguments$getIndices(x, max=0, disallow="NaN") where 'x'
- contains only NA_integer_, would give "Exception: Argument 'x' is
- of length 1 although the range ([0,0]) implies that is should be
- empty." although it should return 'x' as is.
+ o CLEANUP: R CMD check no longer warns on global assignments.
+ o BUG FIX: Arguments$getIndices(x, max = 0, disallow = "NaN") where 'x'
+ contains only NA_integer_, would give "Exception: Argument 'x' is
+ of length 1 although the range ([0,0]) implies that is should be
+ empty." although it should return 'x' as is.
+
+
Version: 1.19.0 [2012-11-29]
-o CLEANUP: Dropped lapply() for MultiVerbose.
-o Added as.list() to MultiVerbose.
+ o CLEANUP: Dropped lapply() for MultiVerbose.
+ o Added as.list() to MultiVerbose.
+
+
Version: 1.18.4 [2012-11-21]
-o Now declaring all S3 methods in the namespace.
-
+ o Now declaring all S3 methods in the namespace.
+
+
Version: 1.18.3 [2012-11-06]
-o BUG FIX: queryRCmdCheck() did not detect "tests" evidences when
- 'R CMD check' was testing multiple architectures.
-
+ o BUG FIX: queryRCmdCheck() did not detect "tests" evidences when
+ 'R CMD check' was testing multiple architectures.
+
+
Version: 1.18.2 [2012-11-04]
-o CLEANUP: Replaced all whichVector() with which(), because the
- latter is now the fastest again.
-o CLEANUP: Dropped pre-R 2.3.0 patch of as.character.hexmode().
-o CLEANUP: Dropped pre-R 2.5.0 patch of Sys.setenv().
-o BUG FIX: The 'columnClasses' header field created by writeDataFrame()
- would contain "integer" for "factor":s. Now using class(x)[1] instead
- of storage.mode(x) to infer column classes.
-o BUG FIX: Despite documented header fields 'createdBy' and 'createdOn'
- to be ignored if NULL, they did set the corresponding' element in
- 'header' argument to NULL if they were NULL.
+ o CLEANUP: Replaced all whichVector() with which(), because the
+ latter is now the fastest again.
-Version: 1.18.1 [2012-10-31]
-o Now gzip()/gunzip()/bunzip2() creates the directory of destination
- pathname 'destfile', iff missing.
+ o CLEANUP: Dropped pre-R 2.3.0 patch of as.character.hexmode().
+
+ o CLEANUP: Dropped pre-R 2.5.0 patch of Sys.setenv().
+
+ o BUG FIX: The 'columnClasses' header field created by writeDataFrame()
+ would contain "integer" for "factor":s. Now using class(x)[1] instead
+ of storage.mode(x) to infer column classes.
+ o BUG FIX: Despite documented header fields 'createdBy' and 'createdOn'
+ to be ignored if NULL, they did set the corresponding' element in
+ 'header' argument to NULL if they were NULL.
+
+
+Version: 1.18.1 [2012-10-31]
+ o Now gzip()/gunzip()/bunzip2() creates the directory of destination
+ pathname 'destfile', iff missing.
+
+
Version: 1.18.0 [2012-10-29]
-o Added trial version of readWindowsShellLink(), which eventually
- will replace readWindowsShortcut().
-o GENERALIZATION: Now filePath() does a better job reading Windows
- Shell Links/Windows Shortcut (*.lnk) files.
-o ROBUSTNESS: Now createWindowsShortcut() uses an improved validation
- strategy of the created *.lnk file.
+ o Added trial version of readWindowsShellLink(), which eventually
+ will replace readWindowsShortcut().
-Version: 1.17.4 [2012-10-26]
-o BUG FIX: example(createWindowsShortcut) could throw an error on
- some systems. The exact reason for this is unknown, so for now
- it's instead generating a warning rather that an error.
+ o GENERALIZATION: Now filePath() does a better job reading Windows
+ Shell Links/Windows Shortcut (*.lnk) files.
+ o ROBUSTNESS: Now createWindowsShortcut() uses an improved validation
+ strategy of the created *.lnk file.
+
+
+Version: 1.17.4 [2012-10-26]
+ o BUG FIX: example(createWindowsShortcut) could throw an error on
+ some systems. The exact reason for this is unknown, so for now
+ it's instead generating a warning rather that an error.
+
+
Version: 1.17.3 [2012-10-26]
-o RECOMMENDATION: Since R v2.11.0, you should use base::which() instead
- of whichVector(), which now help("whichVector") also explains. Also,
- whichVector() was removed from the help index of the package.
-o CRAN POLICY: Made the examples run faster for R CMD check.
+ o RECOMMENDATION: Since R v2.11.0, you should use base::which() instead
+ of whichVector(), which now help("whichVector") also explains. Also,
+ whichVector() was removed from the help index of the package.
+ o CRAN POLICY: Made the examples run faster for R CMD check.
+
+
Version: 1.17.2 [2012-10-21]
-o ROBUSTNESS: Added argument 'maxTries' to Arguments$getWritablePathname()
- to have the method try to create missing directories multiple times
- before giving up. This also means that it will take a longer for
- this method to fail creating a directory.
-o Now Arguments$getWritablePathname() gives a more informative error
- if failed, analogously to Arguments$getReadablePathname().
+ o ROBUSTNESS: Added argument 'maxTries' to Arguments$getWritablePathname()
+ to have the method try to create missing directories multiple times
+ before giving up. This also means that it will take a longer for
+ this method to fail creating a directory.
+ o Now Arguments$getWritablePathname() gives a more informative error
+ if failed, analogously to Arguments$getReadablePathname().
+
+
Version: 1.17.1 [2012-10-19]
-o mkdirs(path) could generate a warning if the path was created
- by another process as a race condition. Now it always checks to
- see if the directory already exists just before trying to create
- the directory.
-
+ o mkdirs(path) could generate a warning if the path was created
+ by another process as a race condition. Now it always checks to
+ see if the directory already exists just before trying to create
+ the directory.
+
+
Version: 1.17.0 [2012-10-16]
-o Moved Arguments$getFilename() from R.filesets to R.utils.
- Added Rd help.
-o ROBUSTNESS: Bumped up package dependencies.
+ o Moved Arguments$getFilename() from R.filesets to R.utils.
+ Added Rd help.
+ o ROBUSTNESS: Bumped up package dependencies.
+
+
Version: 1.16.6 [2012-10-09]
-o BUG FIX: evalWithTimeout() would not reset the time limits after
- returning. Thanks to Gregory Ryslik at Yale University for
- reporting on this.
-
+ o BUG FIX: evalWithTimeout() would not reset the time limits after
+ returning. Thanks to Gregory Ryslik at Yale University for
+ reporting on this.
+
+
Version: 1.16.5 [2012-09-26]
-o Added argument 'skip' to createLink().
-o ROBUSTNESS: Now createLink(..., overwrite=TRUE) will try to undo
- the overwrite, iff it failed to create the new link.
-o BUG FIX: createLink(..., overwrite=TRUE) would give an error saying
- "file already exists" (iff that is true) when it tries to create
- a "unix-symlink" link. Thanks Taku Tokuyasu at UCSF for the report.
+ o Added argument 'skip' to createLink().
-Version: 1.16.4 [2012-09-24]
-o BUG FIX: Arguments$getReadablePath(..., mustExist=FALSE) did not work.
+ o ROBUSTNESS: Now createLink(..., overwrite = TRUE) will try to undo
+ the overwrite, iff it failed to create the new link.
+ o BUG FIX: createLink(..., overwrite = TRUE) would give an error saying
+ "file already exists" (iff that is true) when it tries to create
+ a "unix-symlink" link. Thanks Taku Tokuyasu at UCSF for the report.
+
+
+Version: 1.16.4 [2012-09-24]
+ o BUG FIX: Arguments$getReadablePath(..., mustExist = FALSE) did not work.
+
+
Version: 1.16.3 [2012-09-21]
-o Now insert() silently expands 'values' to be of the same length
- as 'ats', iff length(values) == 1.
-o toCamelCase(..., preserveSameCase=TRUE) makes all-upper-case
- words into same-case words, e.g. toCamelCase("HTML View",
- preserveSameCase=TRUE) outputs "htmlView" (not "hTMLView").
- Added system tests for toCamelCase().
+ o Now insert() silently expands 'values' to be of the same length
+ as 'ats', iff length(values) == 1.
+ o toCamelCase(..., preserveSameCase = TRUE) makes all-upper-case
+ words into same-case words, e.g. toCamelCase("HTML View",
+ preserveSameCase = TRUE) outputs "htmlView" (not "hTMLView").
+ Added system tests for toCamelCase().
+
+
Version: 1.16.2 [2012-09-12]
-o ROBUSTNESS/CRAN POLICY: moveInSearchPath() no longer calls
- .Internal(detach(...)) but instead base::detach() in such a
- way that neither detach hooks nor .Last.lib() are called.
-
+ o ROBUSTNESS/CRAN POLICY: moveInSearchPath() no longer calls
+ .Internal(detach(...)) but instead base::detach() in such a
+ way that neither detach hooks nor .Last.lib() are called.
+
+
Version: 1.16.1 [2012-09-07]
-o Now createLink() also supports targets with '~' in the path.
-o ROBUSTNESS: createLink(target="C:/") would try to create a link with
- name "C:", which is not valid resulting is the somewhat confusing
- error on "cannot symlink 'S:' to 'S:', reason 'Access is denied'".
- Now it instead throws "Cannot infer a valid link name from argument
- 'target': C:/".
-o ROBUSTNESS/BUG FIX: On Windows, it could happen that createLink()
- would generate a zero-size link file that did not link to the target
- as a result of a failed file.symlink(). This is now tested for such
- that if an invalid link file was created, it is removed again.
+ o Now createLink() also supports targets with '~' in the path.
+
+ o ROBUSTNESS: createLink(target = "C:/") would try to create a link with
+ name "C:", which is not valid resulting is the somewhat confusing
+ error on "cannot symlink 'S:' to 'S:', reason 'Access is denied'".
+ Now it instead throws "Cannot infer a valid link name from argument
+ 'target': C:/".
+ o ROBUSTNESS/BUG FIX: On Windows, it could happen that createLink()
+ would generate a zero-size link file that did not link to the target
+ as a result of a failed file.symlink(). This is now tested for such
+ that if an invalid link file was created, it is removed again.
+
+
Version: 1.16.0 [2012-07-11]
-o CLEANUP: Dropped the graphics device related functions that
- were moved to R.devices.
-o System$findGraphicsDevice() no longer tries to create a PNG
- device using png2(), because that has now moved to R.devices.
-o Updated package dependencies.
+ o CLEANUP: Dropped the graphics device related functions that
+ were moved to R.devices.
-Version: 1.15.1 [2012-06-16]
-o Now package only imports/no longer depends on the 'utils' package.
- This means that all packages that depends on 'R.utils' for loading
- 'utils' for them need to explicitly load it themselves.
+ o System$findGraphicsDevice() no longer tries to create a PNG
+ device using png2(), because that has now moved to R.devices.
+ o Updated package dependencies.
+
+
+Version: 1.15.1 [2012-06-16]
+ o Now package only imports/no longer depends on the 'utils' package.
+ This means that all packages that depends on 'R.utils' for loading
+ 'utils' for them need to explicitly load it themselves.
+
+
Version: 1.15.0 [2012-05-22]
-o Added systemR() for launching an external R process.
-o Package no longer loads (via a DESCRIPTION Depends) the
- R.devices package, because that would cause a circular
- package dependency. Instead, we're keeping the graphical
- device functions here until all reverse dependent packages
- have been set to explicitly use R.devices.
+ o Added systemR() for launching an external R process.
+ o Package no longer loads (via a DESCRIPTION Depends) the
+ R.devices package, because that would cause a circular
+ package dependency. Instead, we're keeping the graphical
+ device functions here until all reverse dependent packages
+ have been set to explicitly use R.devices.
+
+
Version: 1.14.0 [2012-05-01]
-o Copied all functions related to graphics devices to new package
- R.devices (v2.1.1), which is now on CRAN. For backward
- compatibility, the R.utils package will for now depend and
- hence load the R.devices package.
-
+ o Copied all functions related to graphics devices to new package
+ R.devices (v2.1.1), which is now on CRAN. For backward
+ compatibility, the R.utils package will for now depend and
+ hence load the R.devices package.
+
+
Version: 1.13.1 [2012-04-16]
-o Added findFiles(), which orginates from the affxparser package.
-
+ o Added findFiles(), which orginates from the affxparser package.
+
+
Version: 1.13.0 [2012-04-07]
-o Added toBMP() and toTIFF().
-
+ o Added toBMP() and toTIFF().
+
+
Version: 1.12.2 [2012-04-05]
-o Now it is possible to have devEval() rename incompletely generated
- image files, by using argument onIncomplete="rename". This will simplify
- troubleshooting. The default is still to remove incomplete files.
-o ROBUSTNESS: Updated package dependencies.
+ o Now it is possible to have devEval() rename incompletely generated
+ image files, by using argument onIncomplete = "rename". This will simplify
+ troubleshooting. The default is still to remove incomplete files.
+ o ROBUSTNESS: Updated package dependencies.
+
+
Version: 1.12.1 [2012-03-20]
-o BUG FIX: .onAttach() would try to call getMessage(ex) on an 'error'
- if there was a problem adding a finalizer, resulting in "no applicable
- method for 'getMessage' applied to an object of class "c('simpleError',
- 'error', 'condition')". Now using 'ex$message' instead.
-
+ o BUG FIX: .onAttach() would try to call getMessage(ex) on an 'error'
+ if there was a problem adding a finalizer, resulting in "no applicable
+ method for 'getMessage' applied to an object of class "c('simpleError',
+ 'error', 'condition')". Now using 'ex$message' instead.
+
+
Version: 1.12.0 [2012-03-08]
-o CRAN POLICY: Renamed remove() for FileProgressBar to cleanup(),
- because otherwise it would be inevitable to create an internal
- copy of base::remove() which contains an .Internal() call.
- This move may break existing code that calls remove() on an
- FileProgressBar object.
-o CRAN POLICY: Removed all internal copies of 'base' and 'utils'
- functions that have .Internal() calls.
-o CLEANUP: Removed relibrary() function, because it has not worked
- properly since R introduced namespaces, which is several years.
+ o CRAN POLICY: Renamed remove() for FileProgressBar to cleanup(),
+ because otherwise it would be inevitable to create an internal
+ copy of base::remove() which contains an .Internal() call.
+ This move may break existing code that calls remove() on an
+ FileProgressBar object.
-Version: 1.11.2 [2012-02-29]
-o CRAN POLICY: Now capture() for Verbose uses withVisible() instead
- of an .Internal(eval.with.vis()) call.
+ o CRAN POLICY: Removed all internal copies of 'base' and 'utils'
+ functions that have .Internal() calls.
+ o CLEANUP: Removed relibrary() function, because it has not worked
+ properly since R introduced namespaces, which is several years.
+
+
+Version: 1.11.2 [2012-02-29]
+ o CRAN POLICY: Now capture() for Verbose uses withVisible() instead
+ of an .Internal(eval.with.vis()) call.
+
+
Version: 1.11.1 [2012-02-28]
-o ROBUSTNESS: The creation of image files by devEval() is now
- close to being "atomic". That is, if the code for plotting the
- figure is interrupted (e.g. by a user interrupt or an error),
- then any created image file is removed. This avoids leaving
- incomplete/blank image files behind.
-
+ o ROBUSTNESS: The creation of image files by devEval() is now
+ close to being "atomic". That is, if the code for plotting the
+ figure is interrupted (e.g. by a user interrupt or an error),
+ then any created image file is removed. This avoids leaving
+ incomplete/blank image files behind.
+
+
Version: 1.11.0 [2012-02-26]
-o GENERALIZATION: Now devOptions() accepts passing a device function
- in addition a string, e.g. devOptions(png) and devOptions("png").
-o Added argument 'scale' to devNew().
-o BUG FIX: Before devNew(..., aspectRatio=1) would ignore
- devOptions(...)$width if neither argument 'width' nor 'height'
- was given.
+ o GENERALIZATION: Now devOptions() accepts passing a device function
+ in addition a string, e.g. devOptions(png) and devOptions("png").
+
+ o Added argument 'scale' to devNew().
+ o BUG FIX: Before devNew(..., aspectRatio = 1) would ignore
+ devOptions(...)$width if neither argument 'width' nor 'height'
+ was given.
+
+
Version: 1.10.0 [2012-02-23]
-o Added swapXY() and draw() for 'density' objects. Used to be
- in the aroma.core package.
-o ROBUSTNESS: Package now explicitly depends on 'utils' and
- 'R.methodsS3'. Before it relied on 'R.oo' to load those.
+ o Added swapXY() and draw() for 'density' objects. Used to be
+ in the aroma.core package.
+ o ROBUSTNESS: Package now explicitly depends on 'utils' and
+ 'R.methodsS3'. Before it relied on 'R.oo' to load those.
+
+
Version: 1.9.11 [2012-01-17]
-o ROBUSTNESS: Now System$findGraphicsDevice() not only assert that
- an image file is generated, but also that its filesize is non-zero.
- This avoids returning a device that generates empty image files.
- Also updated the time out to 10 secs (was 30 secs).
-
+ o ROBUSTNESS: Now System$findGraphicsDevice() not only assert that
+ an image file is generated, but also that its filesize is non-zero.
+ This avoids returning a device that generates empty image files.
+ Also updated the time out to 10 secs (was 30 secs).
+
+
Version: 1.9.10 [2012-01-12]
-o CLEANUP: reassignInPackage() calls function that are considered
- "unsafe" by the new CRAN policies, i.e. unlockBinding() and
- assignInNamespace(). However, we still wish to keep this method
- available to advanced users. In order to avoid getting NOTEs
- from R CMD check, we have "hidden" those unsafe function calls.
-
+ o CLEANUP: reassignInPackage() calls function that are considered
+ "unsafe" by the new CRAN policies, i.e. unlockBinding() and
+ assignInNamespace(). However, we still wish to keep this method
+ available to advanced users. In order to avoid getting NOTEs
+ from R CMD check, we have "hidden" those unsafe function calls.
+
+
Version: 1.9.9 [2012-01-11]
-o BUG FIX: writeRaw() for Verbose would throw error "Trying to coerce
- more than one character string to a GString, which is not supported."
- iff passing a vector of strings.
-
+ o BUG FIX: writeRaw() for Verbose would throw error "Trying to coerce
+ more than one character string to a GString, which is not supported."
+ iff passing a vector of strings.
+
+
Version: 1.9.8 [2011-12-30]
-o DOCUMENTATION: The help now explains that evalWithTimeout(readline())
- does not throw a timeout exception until after readline() returns.
-
+ o DOCUMENTATION: The help now explains that evalWithTimeout(readline())
+ does not throw a timeout exception until after readline() returns.
+
+
Version: 1.9.7 [2011-12-16]
-o BUG FIX: evalWithTimeout() would not detect timeouts in R sessions
- that use a non-English locale.
-o BUG FIX: Now evalWithTimeout(..., onTimeout="silent") works. Thanks
- Nicholas Beeton (Univ. of Tasmania, Australia) for reporting on this.
+ o BUG FIX: evalWithTimeout() would not detect timeouts in R sessions
+ that use a non-English locale.
+ o BUG FIX: Now evalWithTimeout(..., onTimeout = "silent") works. Thanks
+ Nicholas Beeton (Univ. of Tasmania, Australia) for reporting on this.
+
+
Version: 1.9.6 [2011-11-23]
-o BUG FIX: evalCapture() with argument 'envir' defaulting to parent.frame()
- would not be evaluated in the parent frame as it should. It appears
- that the internal capture.output() prevents this from happening, unless
- argument 'envir' is explictly evaluated within evalCapture().
-
+ o BUG FIX: evalCapture() with argument 'envir' defaulting to parent.frame()
+ would not be evaluated in the parent frame as it should. It appears
+ that the internal capture.output() prevents this from happening, unless
+ argument 'envir' is explictly evaluated within evalCapture().
+
+
Version: 1.9.5 [2011-11-19]
-o ROBUSTNESS: Now parse() and as.character() handles "empty" GString:s.
-o ROBUSTNESS: Now GString() asserts that it only holds one string.
+ o ROBUSTNESS: Now parse() and as.character() handles "empty" GString:s.
+ o ROBUSTNESS: Now GString() asserts that it only holds one string.
+
+
Version: 1.9.4 [2011-11-15]
-o SPEEDUP: Now Arguments$getCharacters(s, asGString=TRUE) is much
- faster for elements of 's' that are non-GStrings. For long
- character vectors the speedup is 100-200x times.
-o SPEEDUP: Now as.character() and parse() for GString return
- faster if the string is a plain string without markup etc.
- This made as.character() about 10-15 times faster.
+ o SPEEDUP: Now Arguments$getCharacters(s, asGString = TRUE) is much
+ faster for elements of 's' that are non-GStrings. For long
+ character vectors the speedup is 100-200x times.
+ o SPEEDUP: Now as.character() and parse() for GString return
+ faster if the string is a plain string without markup etc.
+ This made as.character() about 10-15 times faster.
+
+
Version: 1.9.3 [2011-11-07]
-o Added 'quarts' to the list of (possible) devices for devOptions().
-o BUG FIX: devOptions() assumed that all devices exist on
- all platforms, causing it to give an error on some.
+ o Added 'quarts' to the list of (possible) devices for devOptions().
+ o BUG FIX: devOptions() assumed that all devices exist on
+ all platforms, causing it to give an error on some.
+
+
Version: 1.9.2 [2011-11-06]
-o Added evalCapture() for evaluating an expression and
- capturing its deparsed code and/or output.
-
+ o Added evalCapture() for evaluating an expression and
+ capturing its deparsed code and/or output.
+
+
Version: 1.9.1 [2011-11-05]
-o Added toEPS(), toPDF(), toPNG() and toSVG().
-o Added devOptions().
-o Added default 'width' and 'height' values to eps().
-o Turned png2() and jpeg2() into plain functions without a generic.
- This is consistent with how eps() is defined.
-o GENERALIZATION: Now the default 'width' is inferred from
- devOptions() if needed.
-o DOCUMENTATION: Added an example to help(devEval).
+ o Added toEPS(), toPDF(), toPNG() and toSVG().
-Version: 1.9.0 [2011-11-03]
-o Added queryRCmdCheck(), which retrieves the status of 'R CMD check',
- iff it is running.
+ o Added devOptions().
+ o Added default 'width' and 'height' values to eps().
-Version: 1.8.8 [2011-11-01]
-o Added argument 'dims' to extract() for arrays. Also, argument 'drop'
- was moved to the end.
+ o Turned png2() and jpeg2() into plain functions without a generic.
+ This is consistent with how eps() is defined.
+ o GENERALIZATION: Now the default 'width' is inferred from
+ devOptions() if needed.
-Version: 1.8.7 [2011-11-01]
-o CLEANUP: Fixed a R CMD check NOTE that would show up in R v2.15.0 devel.
+ o DOCUMENTATION: Added an example to help(devEval).
+
+
+Version: 1.9.0 [2011-11-03]
+ o Added queryRCmdCheck(), which retrieves the status of 'R CMD check',
+ iff it is running.
+
+
+Version: 1.8.8 [2011-11-01]
-Version: 1.8.6 [2011-10-31]
-o Added argument 'field' to devEval().
+ o Added argument 'dims' to extract() for arrays. Also, argument 'drop'
+ was moved to the end.
+
+
+Version: 1.8.7 [2011-11-01]
+ o CLEANUP: Fixed a R CMD check NOTE that would show up in R v2.15.0 devel.
+
+
+Version: 1.8.6 [2011-10-31]
+ o Added argument 'field' to devEval().
+
+
Version: 1.8.5 [2011-10-16]
-o CORRECTION: Arguments$getNumerics(c(Inf), disallow="Inf") would report
- that it contains "NA" instead of "Inf" values.
-
+ o CORRECTION: Arguments$getNumerics(c(Inf), disallow = "Inf") would report
+ that it contains "NA" instead of "Inf" values.
+
+
Version: 1.8.4 [2011-10-08]
-o Now the default for argument 'methods' of createLink() can be set
- via option "createLink/args/methods".
-
+ o Now the default for argument 'methods' of createLink() can be set
+ via option "createLink/args/methods".
+
+
Version: 1.8.3 [2011-09-30]
-o Added installPackages() for installing R packages by names or URLs.
- This method was previously in the hbLite.R script of braju.com.
-
+ o Added installPackages() for installing R packages by names or URLs.
+ This method was previously in the hbLite.R script of braju.com.
+
+
Version: 1.8.2 [2011-09-24]
-o devNew() no longer gives a warning about argument 'aspectRatio' is
- specified when both or neither of 'width' and 'height' are given,
- and 'aspectRatio' is 1.
-o Internal readDWord() and readQWord() of readWindowsShortcut() would
- try read 4- and 8-byte integers as non-signed, which is not supported
- by base::readBin() and hence instead read as signed integers.
- Starting with R v2.13.1 this would generate a lot of warnings.
+ o devNew() no longer gives a warning about argument 'aspectRatio' is
+ specified when both or neither of 'width' and 'height' are given,
+ and 'aspectRatio' is 1.
+ o Internal readDWord() and readQWord() of readWindowsShortcut() would
+ try read 4- and 8-byte integers as non-signed, which is not supported
+ by base::readBin() and hence instead read as signed integers.
+ Starting with R v2.13.1 this would generate a lot of warnings.
+
+
Version: 1.8.1 [2011-09-19]
-o Now System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and
- System$getMappedDrivesOnWindows() also handles Windows UNC paths
- (i.e. network resource). This was triggered by a discussion with
- Keith Jewell at Campden BRI Group, UK.
-o WORKAROUND: isDirectory("C:/") would not return TRUE due to a
- bug in file.info("C:/") causing it to return NAs.
-o Now attachLocally() returns a character vector also of length
- zero. Before NULL was returned.
+ o Now System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and
+ System$getMappedDrivesOnWindows() also handles Windows UNC paths
+ (i.e. network resource). This was triggered by a discussion with
+ Keith Jewell at Campden BRI Group, UK.
+
+ o WORKAROUND: isDirectory("C:/") would not return TRUE due to a
+ bug in file.info("C:/") causing it to return NAs.
+ o Now attachLocally() returns a character vector also of length
+ zero. Before NULL was returned.
+
+
Version: 1.8.0 [2011-09-14]
-o Added writeDataFrame().
-o ROBUSTNESS: Added sanity checks to example(capitalize).
-o DOCUMENTATION: Improved example(commandArgs).
-o BUG FIX: commandArgs() would not handle '-<key> <value>' and
- '--<key> <value>' properly in all cases.
+ o Added writeDataFrame().
-Version: 1.7.8 [2011-07-24]
-o Undoing v1.7.7 to again exports '.conflicts.OK' in order to avoid
- several warnings when loading package.
+ o ROBUSTNESS: Added sanity checks to example(capitalize).
+ o DOCUMENTATION: Improved example(commandArgs).
-Version: 1.7.7 [2011-07-23]
-o '.conflicts.OK' is no longer exported, because it would cause
- other "downstream" packages to generate a WARNING in R CMD check.
+ o BUG FIX: commandArgs() would not handle '-<key> <value>' and
+ '--<key> <value>' properly in all cases.
+
+
+Version: 1.7.8 [2011-07-24]
+ o Undoing v1.7.7 to again exports '.conflicts.OK' in order to avoid
+ several warnings when loading package.
+
+
+Version: 1.7.7 [2011-07-23]
+ o '.conflicts.OK' is no longer exported, because it would cause
+ other "downstream" packages to generate a WARNING in R CMD check.
+
+
Version: 1.7.6 [2011-04-30]
-o Added isReplicated() and replicates() for identifying entries
- in a vector that are non-unique. Corresponding isSingle() and
- singles() identifies entries that exists only once.
-
+ o Added isReplicated() and replicates() for identifying entries
+ in a vector that are non-unique. Corresponding isSingle() and
+ singles() identifies entries that exists only once.
+
+
Version: 1.7.5 [2011-04-12]
-o Now devEval("jpg", ...) is recognized as devEval("jpeg", ...).
-
+ o Now devEval("jpg", ...) is recognized as devEval("jpeg", ...).
+
+
Version: 1.7.4 [2011-04-03]
-o Now hpaste(..., sep=" ", maxHead=Inf) corresponds to
- paste(..., sep=" ", collapse=", "). Added to example.
-
+ o Now hpaste(..., sep = " ", maxHead = Inf) corresponds to
+ paste(..., sep = " ", collapse = ", "). Added to example.
+
+
Version: 1.7.3 [2011-04-02]
-o Added hpaste() for human-readable pasting, e.g. "1, 2, 3, ..., 10".
-o Now argument 'force' of devEval() defaults to
- getOption("devEval/args/force", TRUE).
+ o Added hpaste() for human-readable pasting, e.g. "1, 2, 3, ..., 10".
+ o Now argument 'force' of devEval() defaults to
+ getOption("devEval/args/force", TRUE).
+
+
Version: 1.7.2 [2011-03-18]
-o Now argument 'path' of devEval() defaults to
- getOption("devEval/args/path", "figures/").
-o Now devEval() does a better job of "cleaning up" 'name' and 'tags'.
+ o Now argument 'path' of devEval() defaults to
+ getOption("devEval/args/path", "figures/").
+ o Now devEval() does a better job of "cleaning up" 'name' and 'tags'.
+
+
Version: 1.7.1 [2011-03-18]
-o devNew() gained option 'devNew/args/par', which can be used to specify
- the default graphical parameters for devNew(). Any additional
- parameters passed via argument 'par' will override such default ones,
- if both specifies the same parameter.
-o The automatic archiving of devEval() is not considered unless
- the R.archive package is loaded, regardless of option settings.
-o DOCUMENTATION: The title of help(devDone) was incorrect.
+ o devNew() gained option 'devNew/args/par', which can be used to specify
+ the default graphical parameters for devNew(). Any additional
+ parameters passed via argument 'par' will override such default ones,
+ if both specifies the same parameter.
+ o The automatic archiving of devEval() is not considered unless
+ the R.archive package is loaded, regardless of option settings.
+
+ o DOCUMENTATION: The title of help(devDone) was incorrect.
+
+
Version: 1.7.0 [2011-03-10]
-o Now argument 'aspectRatio' of devNew() defaults to 1 (not NULL).
-o Added setOption(), the "set version" of getOption().
-o Added env() for creating an environment and evaluating an
- expression inside of it in one go.
-o Added argument 'path' to sourceTo().
-o REPRODUCIBLE RESEARCH: Now devEval() archives any generated
- image files if R.archive option 'devEval' is TRUE.
-o BUG FIX: sourceTo() would not work for URLs.
+ o Now argument 'aspectRatio' of devNew() defaults to 1 (not NULL).
+
+ o Added setOption(), the "set version" of getOption().
+
+ o Added env() for creating an environment and evaluating an
+ expression inside of it in one go.
+ o Added argument 'path' to sourceTo().
+
+ o REPRODUCIBLE RESEARCH: Now devEval() archives any generated
+ image files if R.archive option 'devEval' is TRUE.
+
+ o BUG FIX: sourceTo() would not work for URLs.
+
+
Version: 1.6.6 [2011-03-08]
-o Now Arguments$getWritablePath(NULL) returns NULL without asserting
- write permission, which is analogue to how it is done with
- Arguments$getReadablePath(NULL).
-o Added argument 'timestamp' to printf() for Verbose so that the
- timestamp can be turned off/on explicitly as for cat().
+ o Now Arguments$getWritablePath(NULL) returns NULL without asserting
+ write permission, which is analogue to how it is done with
+ Arguments$getReadablePath(NULL).
+ o Added argument 'timestamp' to printf() for Verbose so that the
+ timestamp can be turned off/on explicitly as for cat().
+
+
Version: 1.6.5 [2011-03-03]
-o Added trial version of createFileAtomically() for creating files
- atomically, by writing to a temporary file which is then renamed.
-o Added trial versions of push-, popBackupFile() for backing up
- and restoring a file.
-o Added trial versions of push-, popTemporaryFile() for working
- toward a temporary file.
-o Added trial version of renameFile(), which to additional
- validation afterward.
+ o Added trial version of createFileAtomically() for creating files
+ atomically, by writing to a temporary file which is then renamed.
-Version: 1.6.4 [2011-02-28]
-o (Incomplete revision submitted to CRAN by mistake)
+ o Added trial versions of push-, popBackupFile() for backing up
+ and restoring a file.
+ o Added trial versions of push-, popTemporaryFile() for working
+ toward a temporary file.
+ o Added trial version of renameFile(), which to additional
+ validation afterward.
+
+
+Version: 1.6.4 [2011-02-28]
+
+ o (Incomplete revision submitted to CRAN by mistake)
+
+
Version: 1.6.3 [2011-02-20]
-o Added argument 'par' to devNew() for applying graphical parameters
- at the same time as the device is opened, which is especially
- useful when using devEval().
-o Changed argument 'force' of devEval() to default to TRUE.
+ o Added argument 'par' to devNew() for applying graphical parameters
+ at the same time as the device is opened, which is especially
+ useful when using devEval().
+ o Changed argument 'force' of devEval() to default to TRUE.
+
+
Version: 1.6.2 [2011-02-14]
-o Added trial version of devEval() for simple creation of images.
-o Added argument 'aspectRatio' to devNew(), which updates/sets
- the 'height' or the 'width', if the one of the other is not given.
+ o Added trial version of devEval() for simple creation of images.
+ o Added argument 'aspectRatio' to devNew(), which updates/sets
+ the 'height' or the 'width', if the one of the other is not given.
+
+
Version: 1.6.1 [2011-02-01]
-o ROBUSTNESS: Now using argument 'fixed' (not 'fix') in regexpr() calls.
-
+ o ROBUSTNESS: Now using argument 'fixed' (not 'fix') in regexpr() calls.
+
+
Version: 1.6.0 [2010-12-07]
-o Added evalWithTimeout().
-
+ o Added evalWithTimeout().
+
+
Version: 1.5.8 [2010-11-21]
-o ROBUSTNESS: Now loadObject() asserts that the file exists. If file
- doesn't exist, an informative error message is thrown.
-o ROBUSTNESS: Now System$mapDriveOnWindows() does not give an error if
- trying to map the same drive letter to the same path multiple times.
-o TYPO: Static methods getVector() and getRegularExpression() of
- Arguments would report the incorrect argument name.
-o BUG FIX: System$mapDriveOnWindows() and System$unmapDriveOnWindows()
- did not work if the path contained a space. Now the path is quoted.
-o BUG FIX: Now removeDirectory() also works for paths starting with
- a tilde (~). The reason was/is that base::unlink() used internally
- does not support that. We now use base::path.expand() first.
+ o ROBUSTNESS: Now loadObject() asserts that the file exists. If file
+ doesn't exist, an informative error message is thrown.
+
+ o ROBUSTNESS: Now System$mapDriveOnWindows() does not give an error if
+ trying to map the same drive letter to the same path multiple times.
+
+ o TYPO: Static methods getVector() and getRegularExpression() of
+ Arguments would report the incorrect argument name.
+ o BUG FIX: System$mapDriveOnWindows() and System$unmapDriveOnWindows()
+ did not work if the path contained a space. Now the path is quoted.
+
+ o BUG FIX: Now removeDirectory() also works for paths starting with
+ a tilde (~). The reason was/is that base::unlink() used internally
+ does not support that. We now use base::path.expand() first.
+
+
Version: 1.5.7 [2010-11-07]
-o ROBUSTNESS: Now read/writeBinFragments() assert that argument 'idxs'
- contains only non-negative indices.
-o Added support to readBinFragments() to start reading from either the
- current file position (default; as previously) or from the start of
- the connection. For backward compatibility, we keep the default to
- be relative to the current position, but this may change in the future.
+ o ROBUSTNESS: Now read/writeBinFragments() assert that argument 'idxs'
+ contains only non-negative indices.
+ o Added support to readBinFragments() to start reading from either the
+ current file position (default; as previously) or from the start of
+ the connection. For backward compatibility, we keep the default to
+ be relative to the current position, but this may change in the future.
+
+
Version: 1.5.6 [2010-11-03]
-o Added resample(), which contrary to sample() also works
- when drawing from a single element.
-
+ o Added resample(), which contrary to sample() also works
+ when drawing from a single element.
+
+
Version: 1.5.5 [2010-10-26]
-o Now argument 'which' to devSet() can be any object. If not a
- single numeric or a single character string, then a checksum
- character string is generated using digest::digest(which).
-
+ o Now argument 'which' to devSet() can be any object. If not a
+ single numeric or a single character string, then a checksum
+ character string is generated using digest::digest(which).
+
+
Version: 1.5.4 [2010-10-13]
-o Now the 'link' argument of createLink() is inferred from the
- 'target' argument if it is "." (or NULL).
-
+ o Now the 'link' argument of createLink() is inferred from the
+ 'target' argument if it is "." (or NULL).
+
+
Version: 1.5.3 [2010-09-29]
-o Added an example to help(findSourceTraceback).
-o BUG FIX: Each entry identified by findSourceTraceback()
- would be duplicated.
+ o Added an example to help(findSourceTraceback).
+ o BUG FIX: Each entry identified by findSourceTraceback()
+ would be duplicated.
+
+
Version: 1.5.2 [2010-09-15]
-o fileAccess() no longer returns a named value if file.access() is used.
-o ROBUSTNESS: Added a more robust test for fileAccess(path, mode=2)
- when 'path' is a directory. Thanks Chao Chen at University of
- Chicago for reporting issues with this.
-o BUG FIX: Now fileAccess(..., mode=1) only utilizes file.info()$exe
- if it is a file and on Windows, otherwise it relies on file.access().
-o DOCUMENTATION: Added an example to help(fileAccess).
-o MISC: Added support for readRdHelp(..., format="text") in R < 2.10.0.
+ o fileAccess() no longer returns a named value if file.access() is used.
+
+ o ROBUSTNESS: Added a more robust test for fileAccess(path, mode = 2)
+ when 'path' is a directory. Thanks Chao Chen at University of
+ Chicago for reporting issues with this.
+
+ o BUG FIX: Now fileAccess(..., mode = 1) only utilizes file.info()$exe
+ if it is a file and on Windows, otherwise it relies on file.access().
+ o DOCUMENTATION: Added an example to help(fileAccess).
+
+ o MISC: Added support for readRdHelp(..., format = "text") in R < 2.10.0.
+
+
Version: 1.5.1 [2010-08-28]
-o Added readRdHelp() for locating and reading installed
- Rd help pages in various formats.
-o Now downloadFile() supports authentication, if 'wget' is
- available on the system.
+ o Added readRdHelp() for locating and reading installed
+ Rd help pages in various formats.
+ o Now downloadFile() supports authentication, if 'wget' is
+ available on the system.
+
+
Version: 1.5.0 [2010-08-04]
-o Added stext(), which previously was in the aroma.core package.
-
+ o Added stext(), which previously was in the aroma.core package.
+
+
Version: 1.4.4 [2010-07-05]
-o Now arrayIndex() returns an @integer @matrix.
-o DOCUMENTATION: Now the help of arrayIndex() links to the
- new arrayInd() in the base package.
+ o Now arrayIndex() returns an @integer @matrix.
+ o DOCUMENTATION: Now the help of arrayIndex() links to the
+ new arrayInd() in the base package.
+
+
Version: 1.4.3 [2010-06-23]
-o BUG FIX: getAbsolutePath("//server/dir/") would incorrectly drop
- the initial double-slashes ('//') and return "/server/dir/".
- Thanks Richard Cotton at Health and Safety Laboratory (HSL), UK,
- for reporting this.
-
+ o BUG FIX: getAbsolutePath("//server/dir/") would incorrectly drop
+ the initial double-slashes ('//') and return "/server/dir/".
+ Thanks Richard Cotton at Health and Safety Laboratory (HSL), UK,
+ for reporting this.
+
+
Version: 1.4.2 [2010-06-09]
-o Added printf(), as a convenient wrapper for cat(sprintf(...)).
-
+ o Added printf(), as a convenient wrapper for cat(sprintf(...)).
+
+
Version: 1.4.1 [2010-05-26]
-o Added downloadFile() for safer and more convenient downloads.
-
+ o Added downloadFile() for safer and more convenient downloads.
+
+
Version: 1.4.0 [2010-03-24]
-o Now R.utils requires R v2.5.0 (circa 2007) or newer. This
- is because there was a change in base::parse() from R v2.4.1
- and R v2.5.0. See news for R.utils v0.9.3.
-o Added a NAMESPACE.
+ o Now R.utils requires R v2.5.0 (circa 2007) or newer. This
+ is because there was a change in base::parse() from R v2.4.1
+ and R v2.5.0. See news for R.utils v0.9.3.
+ o Added a NAMESPACE.
+
+
Version: 1.3.4 [2010-03-02]
-o Added alpha version of an onGarbageCollect() method.
-o BUG FIX: findSourceTraceback() stopped working; probably due to some
- recent updates in base::source().
+ o Added alpha version of an onGarbageCollect() method.
+ o BUG FIX: findSourceTraceback() stopped working; probably due to some
+ recent updates in base::source().
+
+
Version: 1.3.3 [2010-01-25]
-o ROBUSTNESS: Added validation of argument 'range' in Arguments methods.
-
+ o ROBUSTNESS: Added validation of argument 'range' in Arguments methods.
+
+
Version: 1.3.2 [2010-01-09]
-o sourceTo(..., modifiedOnly=FALSE) followed by a sourceTo(...,
- modifiedOnly=TRUE) will now work as expected. Before you had to
- do at least one modifiedOnly=TRUE call before for it to work.
-o sourceTo() no longer gives a warning if there is a missing EOL.
+ o sourceTo(..., modifiedOnly = FALSE) followed by a sourceTo(...,
+ modifiedOnly = TRUE) will now work as expected. Before you had to
+ do at least one modifiedOnly = TRUE call before for it to work.
+ o sourceTo() no longer gives a warning if there is a missing EOL.
+
+
Version: 1.3.1 [2010-01-08]
-o Added System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and
- System$getMappedDrivesOnWindows() for associating drive letters
- with paths on Windows.
-
+ o Added System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and
+ System$getMappedDrivesOnWindows() for associating drive letters
+ with paths on Windows.
+
+
Version: 1.3.0 [2010-01-02]
-o Added argument 'max' to Arguments$getIndices().
-o Added Arguments$getInstanceOf(...).
-o Now Arguments$getWritablePath() and Arguments$getWritablePathname()
- throws an error is an NA file/directory is specified.
-o Now Arguments$getReadablePath() and Arguments$getReadablePathname()
- throws an error is an NA file/directory is specified, unless
- 'mustExist' is FALSE.
-o Moved private GenericSummary from aroma.core to R.utils.
-o ROBUSTNESS: Now getParent(), getAbsolutePath() and getRelativePath()
- returns a (character) NA if the input is NA.
-o ROBUSTNESS: Any NA arguments in '...' to filePath(...) would be parsed
- as "NA" resulting in paths such as "NA/foo/NA" (just as file.path()
- does it). Now a (character) NA is returned.
-o BUG FIX: The example(GString) code escaped a backslash incorrectly.
-o BUG FIX: Arguments$getCharacters(s) would return a *logical* instead
- of a *character* vector if 's' contained all NAs.
-o BUG FIX: Now isFile(NA) and isDirectory(NA) return FALSE.
- Before it gave an unexpected error.
+ o Added argument 'max' to Arguments$getIndices().
-Version: 1.2.6 [2009-12-19]
-o Added argument envir=new.env() to loadToEnv().
+ o Added Arguments$getInstanceOf(...).
+ o Now Arguments$getWritablePath() and Arguments$getWritablePathname()
+ throws an error is an NA file/directory is specified.
-Version: 1.2.5 [2009-11-20]
-o If 'x' is a logical vector, Arguments$getIndices(x) will now return
- the same as if x <- which(x).
+ o Now Arguments$getReadablePath() and Arguments$getReadablePathname()
+ throws an error is an NA file/directory is specified, unless
+ 'mustExist' is FALSE.
+
+ o Moved private GenericSummary from aroma.core to R.utils.
+
+ o ROBUSTNESS: Now getParent(), getAbsolutePath() and getRelativePath()
+ returns a (character) NA if the input is NA.
+
+ o ROBUSTNESS: Any NA arguments in '...' to filePath(...) would be parsed
+ as "NA" resulting in paths such as "NA/foo/NA" (just as file.path()
+ does it). Now a (character) NA is returned.
+ o BUG FIX: The example(GString) code escaped a backslash incorrectly.
+ o BUG FIX: Arguments$getCharacters(s) would return a *logical* instead
+ of a *character* vector if 's' contained all NAs.
+
+ o BUG FIX: Now isFile(NA) and isDirectory(NA) return FALSE.
+ Before it gave an unexpected error.
+
+
+Version: 1.2.6 [2009-12-19]
+
+ o Added argument envir = new.env() to loadToEnv().
+
+
+Version: 1.2.5 [2009-11-20]
+
+ o If 'x' is a logical vector, Arguments$getIndices(x) will now return
+ the same as if x <- which(x).
+
+
Version: 1.2.4 [2009-10-30]
-o ROBUSTIFICATION: Lowered the risk for saveObject() to leave an
- incomplete file due to say power failures etc. This is done by
- first writing to a temporary file, which is then renamed. If the
- temporary file already exists, an exception is thrown.
-o ROBUSTIFICATION: Now Arguments$getWritablePathname(path) validates
- that there is enough file permissions so that a file can be created
- in the 'path' directory.
-o CLEAN UP: On Windows Vista, createLink() produced a stderr message
- "You do not have sufficient privilege to perform this operation", when
- trying to use Windows 'mklink' command. Those message are now silenced.
+ o ROBUSTIFICATION: Lowered the risk for saveObject() to leave an
+ incomplete file due to say power failures etc. This is done by
+ first writing to a temporary file, which is then renamed. If the
+ temporary file already exists, an exception is thrown.
-Version: 1.2.3 [2009-10-20]
-o Added findSourceTraceback(), which finds the pathnames of all
- files currently being source():ed.
+ o ROBUSTIFICATION: Now Arguments$getWritablePathname(path) validates
+ that there is enough file permissions so that a file can be created
+ in the 'path' directory.
+ o CLEAN UP: On Windows Vista, createLink() produced a stderr message
+ "You do not have sufficient privilege to perform this operation", when
+ trying to use Windows 'mklink' command. Those message are now silenced.
+
+
+Version: 1.2.3 [2009-10-20]
+ o Added findSourceTraceback(), which finds the pathnames of all
+ files currently being source():ed.
+
+
Version: 1.2.2 [2009-10-16]
-o Some cleanup of Rd files to meet the stricter requirements.
-
+ o Some cleanup of Rd files to meet the stricter requirements.
+
+
Version: 1.2.1 [2009-10-03]
-o Added createLink().
-o Added createWindowsShortcut(). Currently it only works on Windows
- and version of Windows that runs VB scripts.
+ o Added createLink().
+ o Added createWindowsShortcut(). Currently it only works on Windows
+ and version of Windows that runs VB scripts.
+
+
Version: 1.2.0 [2009-09-09]
-o Fixed broken/missing Rd links.
-
+ o Fixed broken/missing Rd links.
+
+
Version: 1.1.9 [2009-06-29]
-o Added argument 'useNames=FALSE' to getCharacters() of Arguments.
- For forgotten reasons, before (the default now) 'names' attributes
- were always dropped. Now they can be kept, if wanted.
-o Added dimNA<-().
+ o Added argument 'useNames = FALSE' to getCharacters() of Arguments.
+ For forgotten reasons, before (the default now) 'names' attributes
+ were always dropped. Now they can be kept, if wanted.
+ o Added dimNA<-().
+
+
Version: 1.1.8 [2009-06-07]
-o BUG FIX: getParent(..., depth=0) gave an error, instead of returning
- the input path.
-
+ o BUG FIX: getParent(..., depth = 0) gave an error, instead of returning
+ the input path.
+
+
Version: 1.1.7 [2009-05-30]
-o BUG FIX: Argument 'dThreshold' of less() for Verbose had to be named
- in order to be mapped.
-
+ o BUG FIX: Argument 'dThreshold' of less() for Verbose had to be named
+ in order to be mapped.
+
+
Version: 1.1.6 [2009-05-19]
-o UPDATE: Now getEnvironment(), getRegularExpression(), and
- getReadablePathname() give clearer error messages if more the input
- contains more than one element.
-o Now Arguments$getWritablePathname() better explains why a file cannot
- be opened for creation/modification due to wrong file permissions.
+ o UPDATE: Now getEnvironment(), getRegularExpression(), and
+ getReadablePathname() give clearer error messages if more the input
+ contains more than one element.
+ o Now Arguments$getWritablePathname() better explains why a file cannot
+ be opened for creation/modification due to wrong file permissions.
+
+
Version: 1.1.5 [2009-05-16]
-o Changed argument 'asMode' for Arguments$getNumerics() to default to
- NULL instead of "numeric". This will case the method to return integer
- if the input is integer, and double if the input is double. The
- previous default was alway returning doubles, cf. notes on common
- misconception of how as.numeric() works. In the case when the input
- is neither integer or double, the default is to coerce to doubles.
-
+ o Changed argument 'asMode' for Arguments$getNumerics() to default to
+ NULL instead of "numeric". This will case the method to return integer
+ if the input is integer, and double if the input is double. The
+ previous default was alway returning doubles, cf. notes on common
+ misconception of how as.numeric() works. In the case when the input
+ is neither integer or double, the default is to coerce to doubles.
+
+
Version: 1.1.4 [2009-04-04]
-o Now getReadablePathname(..., mustExist=TRUE) of Arguments reports also
- the working directory if the a relative pathname is missing.
-o BUG FIX: getReadablePathname(..., mustExist=TRUE) of Arguments gave an
- internal error if the pathname was in the current directory and did
- not exist.
+ o Now getReadablePathname(..., mustExist = TRUE) of Arguments reports also
+ the working directory if the a relative pathname is missing.
+ o BUG FIX: getReadablePathname(..., mustExist = TRUE) of Arguments gave an
+ internal error if the pathname was in the current directory and did
+ not exist.
+
+
Version: 1.1.3 [2009-01-12]
-o Added isPackageInstalled().
-o FIXUP: There were some Rd warnings with the new R v2.9.0.
+ o Added isPackageInstalled().
+ o FIXUP: There were some Rd warnings with the new R v2.9.0.
+
+
Version: 1.1.2 [2008-12-27]
-o Now getReadablePathname(..., mustExist=TRUE) and
- getWritablePathname(..., mkdirs=FALSE) of Arguments report which
- of the parent directories exists when the requested pathname is not
- found. This will help troubleshooting missing pathnames.
-o Added removeDirectory() for a convenient and safe way to remove
- directories.
-o Added argument 'useNames' to insert(), which is now aware of names
- of the input object.
-o Added subplots() originating from (obsolete) R.graphics.
+ o Now getReadablePathname(..., mustExist = TRUE) and
+ getWritablePathname(..., mkdirs = FALSE) of Arguments report which
+ of the parent directories exists when the requested pathname is not
+ found. This will help troubleshooting missing pathnames.
+ o Added removeDirectory() for a convenient and safe way to remove
+ directories.
+
+ o Added argument 'useNames' to insert(), which is now aware of names
+ of the input object.
+
+ o Added subplots() originating from (obsolete) R.graphics.
+
+
Version: 1.1.1 [2008-12-03]
-o Now getReadablePathname() and getWritablePathname() of Arguments,
- and sourceTo() use the more trusted fileAccess() instead of
- file.access() of 'base'. This will hopefully solve some problems
- where these methods incorrectly gives an error reporting lack of
- file permissions; this could happen when some OSs mounted to other
- external file systems.
-o Added fileAccess() which is intended to give tries harder than
- file.access() to infer file permissions.
-o STABILITY: Added balance and sanity checks for exit() of Verbose.
-o Now gzip() and gunzip() removes the partially written output file if
- the process is interrupted.
-o BUG FIX: readWindowsShortcut() would not work with some Windows
- shortcut files linking to a Windows network file system and generated
- on Windows Vista. Their "flags" in the file headers had more than
- the 8 known bits, which was reported as a file format error. Although
- we don't know what these unknown bits are for, we now accept them
- quitely accepted so at least the known part of the file format is
- returned.
-o BUG FIX: filePath("\\\\shared/foo") would return "\\shared/foo".
+ o Now getReadablePathname() and getWritablePathname() of Arguments,
+ and sourceTo() use the more trusted fileAccess() instead of
+ file.access() of 'base'. This will hopefully solve some problems
+ where these methods incorrectly gives an error reporting lack of
+ file permissions; this could happen when some OSs mounted to other
+ external file systems.
-Version: 1.1.0 [2008-10-24]
-o Now sourceDirectory() also searches for source files with extensions
- *.r, *.q, *.s, and *.S, cf. R manual 'Writing R Extensions'.
+ o Added fileAccess() which is intended to give tries harder than
+ file.access() to infer file permissions.
+ o STABILITY: Added balance and sanity checks for exit() of Verbose.
-Version: 1.0.9 [2008-10-17]
-o BUG FIX: commandArgs() would 'Error in !attr(args, "isEnvVars") :
- invalid argument type' if both arguments excludeReserved=TRUE and
- excludeEnvVars=TRUE were used.
+ o Now gzip() and gunzip() removes the partially written output file if
+ the process is interrupted.
+
+ o BUG FIX: readWindowsShortcut() would not work with some Windows
+ shortcut files linking to a Windows network file system and generated
+ on Windows Vista. Their "flags" in the file headers had more than
+ the 8 known bits, which was reported as a file format error. Although
+ we don't know what these unknown bits are for, we now accept them
+ quitely accepted so at least the known part of the file format is
+ returned.
+
+ o BUG FIX: filePath("\\\\shared/foo") would return "\\shared/foo".
+
+
+Version: 1.1.0 [2008-10-24]
+ o Now sourceDirectory() also searches for source files with extensions
+ *.r, *.q, *.s, and *.S, cf. R manual 'Writing R Extensions'.
+
+
+Version: 1.0.9 [2008-10-17]
+ o BUG FIX: commandArgs() would 'Error in !attr(args, "isEnvVars") :
+ invalid argument type' if both arguments excludeReserved = TRUE and
+ excludeEnvVars = TRUE were used.
+
+
Version: 1.0.8 [2008-10-16]
-o Now devDone(which=1) does nothing. Before it gave an error.
-o BUG FIX: Argument 'type' of devNew() did not take function:s.
+ o Now devDone(which = 1) does nothing. Before it gave an error.
+ o BUG FIX: Argument 'type' of devNew() did not take function:s.
+
+
Version: 1.0.7 [2008-09-20]
-o Added mapToIntervals(), inAnyInterval(), and mergeIntervals().
-
+ o Added mapToIntervals(), inAnyInterval(), and mergeIntervals().
+
+
Version: 1.0.6 [2008-09-08]
-o Now devNew() filters out arguments 'file' and 'filename' if the
- device is interactive.
-
+ o Now devNew() filters out arguments 'file' and 'filename' if the
+ device is interactive.
+
+
Version: 1.0.5 [2008-08-04]
-o Now commandArgs(...) pass '...' to base::commandArgs() making it
- fully backward compatible. It is also updated to recognize all
- R command line options as of R v2.7.1 and R v2.8.0 devel.
-
+ o Now commandArgs(...) pass '...' to base::commandArgs() making it
+ fully backward compatible. It is also updated to recognize all
+ R command line options as of R v2.7.1 and R v2.8.0 devel.
+
+
Version: 1.0.4 [2008-08-01]
-o Now sourceDirectory() is guaranteed to source directories and files
- in lexicographic order.
-o Added countLines() for counting number of lines in a text file.
-o Added several functions for extending the current functions dealing
- with devices. All added functions can address a device by a label
- in addition to the standard device index. The devGetLabel() and
- devSetLabel() gets and sets the label of a give device. devList()
- lists the indices of existing device named by their labels, cf.
- dev.list(). The functions devSet() and devOff() work like
- dev.set() and dev.off() but accept labels as well. Furthermore,
- devSet(idx) will open a device with index 'idx' if it does not
- exists, and devSet(label) a device with that label if not already
- opened. The devIsOpen() checks if a device is open or not. The
- devDone() function calls devOff() except for screen devices.
-
+ o Now sourceDirectory() is guaranteed to source directories and files
+ in lexicographic order.
+
+ o Added countLines() for counting number of lines in a text file.
+
+ o Added several functions for extending the current functions dealing
+ with devices. All added functions can address a device by a label
+ in addition to the standard device index. The devGetLabel() and
+ devSetLabel() gets and sets the label of a give device. devList()
+ lists the indices of existing device named by their labels, cf.
+ dev.list(). The functions devSet() and devOff() work like
+ dev.set() and dev.off() but accept labels as well. Furthermore,
+ devSet(idx) will open a device with index 'idx' if it does not
+ exists, and devSet(label) a device with that label if not already
+ opened. The devIsOpen() checks if a device is open or not. The
+ devDone() function calls devOff() except for screen devices.
+
+
Version: 1.0.3 [2008-07-10]
-o Added readBinFragments() and writeBinFragments() to read and write
- binary data scattered across a connection or a file. These methods
- moved from the R.huge package.
-o Added intervalsToSeq(), which is bijective to seqToIntervals().
-o Added whichVector(), which is almost twice as fast which() for
- logical vectors, especially when there are no missing values.
-o IMPROVEMENT: Major speed up of seqToIntervals().
-o Added gzip().
-o Renamed inst/HISTORY to inst/NEWS according to new R standards.
-o CLEAN UP: as.character() for 'hexmode' is only added if missing.
-o BETA: Added (for now internal) toAsciiRegExprPattern().
+ o Added readBinFragments() and writeBinFragments() to read and write
+ binary data scattered across a connection or a file. These methods
+ moved from the R.huge package.
-Version: 1.0.2 [2008-03-31]
-o BUG FIX: If 'x' in insert(x, ...) had zero length, an
- "Error in from:to : NA/NaN argument" was thrown.
+ o Added intervalsToSeq(), which is bijective to seqToIntervals().
+ o Added whichVector(), which is almost twice as fast which() for
+ logical vectors, especially when there are no missing values.
-Version: 1.0.1 [2008-03-06]
-o BUG FIX: Regular expression pattern 'a-Z' is illegal on (at least)
- some locale, e.g. 'C' (where 'A-z' works). The only way to specify
- the ASCII alphabet is to list all characters explicitly, which we now
- do in all methods of the package. See the r-devel thread
- "invalid regular expression '[a-Z]'" on 2008-03-05 for details.
+ o IMPROVEMENT: Major speed up of seqToIntervals().
+
+ o Added gzip().
+ o Renamed inst/HISTORY to inst/NEWS according to new R standards.
+
+ o CLEAN UP: as.character() for 'hexmode' is only added if missing.
+
+ o BETA: Added (for now internal) toAsciiRegExprPattern().
+
+
+Version: 1.0.2 [2008-03-31]
+ o BUG FIX: If 'x' in insert(x, ...) had zero length, an
+ "Error in from:to : NA/NaN argument" was thrown.
+
+
+Version: 1.0.1 [2008-03-06]
+
+ o BUG FIX: Regular expression pattern 'a-Z' is illegal on (at least)
+ some locale, e.g. 'C' (where 'A-z' works). The only way to specify
+ the ASCII alphabet is to list all characters explicitly, which we now
+ do in all methods of the package. See the r-devel thread
+ "invalid regular expression '[a-Z]'" on 2008-03-05 for details.
+
+
Version: 1.0.0 [2008-02-26]
-o Added touchFile() for updating the timestamp of a file.
-o Added colClasses() for creating "colClasses" vectors.
-o Added isPackageLoaded().
-o The default filename for eps() had extension *.ps not *.eps.
-o Cleaned out empty sections from the Rd help pages.
-o Now the '...' arguments to Arguments$getVerbose() are passed
- to the constructor of Verbose. This allows constructs such
- as Arguments$getVerbose(-10, timestamp=TRUE).
-o BUG FIX: When argument 'values' of insert() was a non-list
- its values were placed in a single-element list even when
- 'ats' contained more than one element. Should have been
- as.list() in those cases.
+ o Added touchFile() for updating the timestamp of a file.
+
+ o Added colClasses() for creating "colClasses" vectors.
+
+ o Added isPackageLoaded().
+
+ o The default filename for eps() had extension *.ps not *.eps.
+ o Cleaned out empty sections from the Rd help pages.
+
+ o Now the '...' arguments to Arguments$getVerbose() are passed
+ to the constructor of Verbose. This allows constructs such
+ as Arguments$getVerbose(-10, timestamp = TRUE).
+
+ o BUG FIX: When argument 'values' of insert() was a non-list
+ its values were placed in a single-element list even when
+ 'ats' contained more than one element. Should have been
+ as.list() in those cases.
+
+
Version: 0.9.8 [2007-11-26]
-o Added copyFile() which safely copies a file by copying to a
- temporary file, which is then renamed.
-o Added isEof() for connections to test for "End of File".
-o Added reassignInPackage().
-o Added dataFrame(), which allocated a data frame of given size
- and column classes.
-o BUG FIX: writeRaw() of MultiVerbose returned a list of logicals.
- Now it returns TRUE (invisibly).
+ o Added copyFile() which safely copies a file by copying to a
+ temporary file, which is then renamed.
-Version: 0.9.7 [2007-09-17]
-o BUG FIX/WORKAROUND: moveInSearchPath() would make the package
- environment loose the 'path' attribute, which is for instance is
- needed by packageDescription(). This would in turn cause
- sessionInfo() to throw an error. Now moveInSearchPath() makes sure
- to set all attributes on a moved package environment to what it
- used to be.
+ o Added isEof() for connections to test for "End of File".
+ o Added reassignInPackage().
+
+ o Added dataFrame(), which allocated a data frame of given size
+ and column classes.
+
+ o BUG FIX: writeRaw() of MultiVerbose returned a list of logicals.
+ Now it returns TRUE (invisibly).
+
+
+Version: 0.9.7 [2007-09-17]
+ o BUG FIX/WORKAROUND: moveInSearchPath() would make the package
+ environment loose the 'path' attribute, which is for instance is
+ needed by packageDescription(). This would in turn cause
+ sessionInfo() to throw an error. Now moveInSearchPath() makes sure
+ to set all attributes on a moved package environment to what it
+ used to be.
+
+
Version: 0.9.6 [2007-08-29]
-o Made documentation for saveObject() and loadObject() public.
-o Now the startup message when loading the package is generated with
- packageStartupMessage() so that it can be suppressed.
-o Added flush() to TextStatusBar. Added flush() to example(TextStatusBar)
- so it displays correctly on Rgui on Windows.
-o Added bunzip2(), cf. gunzip().
-o Added argument 'remove' to gunzip().
-o BUG FIX: There was a typo in readWindowsShortcut() causing field
- 'iconFilename' to potentially be invalid. Thanks Tony Plate for
- reporting this.
+ o Made documentation for saveObject() and loadObject() public.
+ o Now the startup message when loading the package is generated with
+ packageStartupMessage() so that it can be suppressed.
+
+ o Added flush() to TextStatusBar. Added flush() to example(TextStatusBar)
+ so it displays correctly on Rgui on Windows.
+
+ o Added bunzip2(), cf. gunzip().
+
+ o Added argument 'remove' to gunzip().
+
+ o BUG FIX: There was a typo in readWindowsShortcut() causing field
+ 'iconFilename' to potentially be invalid. Thanks Tony Plate for
+ reporting this.
+
+
Version: 0.9.5 [2007-06-09]
-o Updated code to pass the more strict R CMD check R v2.6.0.
-o BUG FIX: Used omit.na() instead of na.omit() in static method
- parseDebian() of System.
+ o Updated code to pass the more strict R CMD check R v2.6.0.
+ o BUG FIX: Used omit.na() instead of na.omit() in static method
+ parseDebian() of System.
+
+
Version: 0.9.4 [2007-05-10]
-o BUG FIX: readTable() tried to access base::read.table() but that was
- moved to 'utils' as of R v2.5.0.
-
+ o BUG FIX: readTable() tried to access base::read.table() but that was
+ moved to 'utils' as of R v2.5.0.
+
+
Version: 0.9.3 [2007-05-09]
-o BUG FIX: Using the R v2.4.x build of R.utils in R v2.5.0 gives
- "Error in parse.default(text = src) : 4 arguments passed to
- 'parse' which requires 6". This is because the internal call
- in base::parse() use different sets of arguments in R v2.4.1
- and R v2.5.0. The fix was to dynamically assign patch.default()
- when the package is loaded.
-
+ o BUG FIX: Using the R v2.4.x build of R.utils in R v2.5.0 gives
+ "Error in parse.default(text = src) : 4 arguments passed to
+ 'parse' which requires 6". This is because the internal call
+ in base::parse() use different sets of arguments in R v2.4.1
+ and R v2.5.0. The fix was to dynamically assign patch.default()
+ when the package is loaded.
+
+
Version: 0.9.2 [2007-04-26]
-o Added trial version of a MultiVerbose class. With this class it
- is possible to write verbose output via multiple Verbose objects
- through one MultiVerbose object, e.g. writing to standard output
- and to log file at the same time.
-
+ o Added trial version of a MultiVerbose class. With this class it
+ is possible to write verbose output via multiple Verbose objects
+ through one MultiVerbose object, e.g. writing to standard output
+ and to log file at the same time.
+
+
Version: 0.9.1 [2007-04-12]
-o BUG FIX: findGhostscript() would give error "paste(path0, collapse
- = ", ") : object "path0" not found" on Windows if Ghostscript was
- not found. This error was caught by CRAN. These problems have
- not been detected locally where Ghostscript is installed.
-
+ o BUG FIX: findGhostscript() would give error "paste(path0, collapse
+ = ", ") : object "path0" not found" on Windows if Ghostscript was
+ not found. This error was caught by CRAN. These problems have
+ not been detected locally where Ghostscript is installed.
+
+
Version: 0.9.0 [2007-04-11]
-o BUG FIX: findGhostscript() of System would give error on
- "invalid subscript type" if non of the paths to be searched exist.
- This error was caught by CRAN.
-
+ o BUG FIX: findGhostscript() of System would give error on
+ "invalid subscript type" if non of the paths to be searched exist.
+ This error was caught by CRAN.
+
+
Version: 0.8.9 [2007-04-07]
-o Removed never needed require(R.io) in openBrowser() for System.
-
+ o Removed never needed require(R.io) in openBrowser() for System.
+
+
Version: 0.8.8 [2007-04-03]
-o Added saveObject() and loadObject().
-o Removed the warning in getRelativePath() about "Cannot infer
- relative pathname, because the two pathnames are not refering
- to the same root/device". The warning was more confusing than
- helpful.
-o BUG FIX: getAbsolutePath("C:/foo/", expandTilde=TRUE) would return
- "C://foo" and not "C:/foo". Now the method also replace all
- multiple occurances of slashes with a single one. This bug
- cause getRelativePath("C:/foo", "C:/") to return the wrong thing.
-o BUG FIX: toCamelCase(toCamelCase(s)) would not be equal to
- toCamelCase(s), but instead result in all lower case letters.
-o BUG FIX: Default value of argument 'format' of timestamp()
- was invalid.
+ o Added saveObject() and loadObject().
+
+ o Removed the warning in getRelativePath() about "Cannot infer
+ relative pathname, because the two pathnames are not refering
+ to the same root/device". The warning was more confusing than
+ helpful.
+
+ o BUG FIX: getAbsolutePath("C:/foo/", expandTilde = TRUE) would return
+ "C://foo" and not "C:/foo". Now the method also replace all
+ multiple occurances of slashes with a single one. This bug
+ cause getRelativePath("C:/foo", "C:/") to return the wrong thing.
+ o BUG FIX: toCamelCase(toCamelCase(s)) would not be equal to
+ toCamelCase(s), but instead result in all lower case letters.
+
+ o BUG FIX: Default value of argument 'format' of timestamp()
+ was invalid.
+
+
Version: 0.8.7 [2007-03-24]
-o Added moveInSearchPath() to reshuffle the search path. Useful
- to change the order of packages after they have loaded.
-o Added toCamelCase() to convert strings.
-o Added loadToEnv() for loading saved data to a new environment.
-o The warning message on "cannot refer relative pathname" for
- getRelativePath() didn't paste the path resulting in a funny
- looking warning.
+ o Added moveInSearchPath() to reshuffle the search path. Useful
+ to change the order of packages after they have loaded.
-Version: 0.8.6 [2007-02-27]
-o An R.utils (v0.8.4) modified .Last() function saved in .RData from
- previous R sessions will be updated with the new modifactions
- according to R.utils v0.8.5.
+ o Added toCamelCase() to convert strings.
+
+ o Added loadToEnv() for loading saved data to a new environment.
+ o The warning message on "cannot refer relative pathname" for
+ getRelativePath() didn't paste the path resulting in a funny
+ looking warning.
+
+
+Version: 0.8.6 [2007-02-27]
+ o An R.utils (v0.8.4) modified .Last() function saved in .RData from
+ previous R sessions will be updated with the new modifactions
+ according to R.utils v0.8.5.
+
+
Version: 0.8.5 [2007-02-26]
-o Added argument 'depth' to getParent().
-o BUG FIX: Added tryCatch() and explicit check for finalizeSession().
- Otherwise if, under special circumstance, one might get the error
- 'Error in .Last() : could not find function "finalizeSession"' when
- trying to quit R with quit(). Thanks Elizabeth Purdum at UC Berkeley
- for reporting this.
-o When running R v2.5.0, Sys.getenv() is used instead of deprecated
- Sys.putenv().
+ o Added argument 'depth' to getParent().
-Version: 0.8.4 [2007-01-10]
-o Now System$findGhostscript() searches all 'Program Files' directories
- too, if on Windows.
+ o BUG FIX: Added tryCatch() and explicit check for finalizeSession().
+ Otherwise if, under special circumstance, one might get the error
+ 'Error in .Last() : could not find function "finalizeSession"' when
+ trying to quit R with quit(). Thanks Elizabeth Purdum at UC Berkeley
+ for reporting this.
+ o When running R v2.5.0, Sys.getenv() is used instead of deprecated
+ Sys.putenv().
+
+
+Version: 0.8.4 [2007-01-10]
+ o Now System$findGhostscript() searches all 'Program Files' directories
+ too, if on Windows.
+
+
Version: 0.8.3 [2006-11-10]
-o Added arrayIndex() to get the multi-dimensional index of an array
- from a one-dimensional index.
-
+ o Added arrayIndex() to get the multi-dimensional index of an array
+ from a one-dimensional index.
+
+
Version: 0.8.2 [2006-10-05]
-o Added popMessage() to TextStatusBar. See example().
-o Added argument 'modifiedOnly' to sourceTo() so that a file is only
- sourced if it has been modified since the last call. Note that this
- argument is passed on by sourceDirectory() too.
+ o Added popMessage() to TextStatusBar. See example().
+ o Added argument 'modifiedOnly' to sourceTo() so that a file is only
+ sourced if it has been modified since the last call. Note that this
+ argument is passed on by sourceDirectory() too.
+
+
Version: 0.8.1 [2006-09-16]
-o BUG FIX: sourceDirectory(..., onError="error") would quietly ignore
- errors in source().
-o Added methods more() and less() to the Verbose class.
+ o BUG FIX: sourceDirectory(..., onError = "error") would quietly ignore
+ errors in source().
+ o Added methods more() and less() to the Verbose class.
+
+
Version: 0.8.0 [2006-08-21]
-o Added isOpen() to check if there is another connection opened to
- a specific file.
-o pushState() of Verbose generated an unnecessary warning due to
- a typo.
+ o Added isOpen() to check if there is another connection opened to
+ a specific file.
+ o pushState() of Verbose generated an unnecessary warning due to
+ a typo.
+
+
Version: 0.7.9 [2006-07-17]
-o The capture() method in Verbose modified a text connection while it was
- still open; from R v2.4.0 this is not allowed. Thanks Brian Ripley for
- pointing this out.
-
+ o The capture() method in Verbose modified a text connection while it was
+ still open; from R v2.4.0 this is not allowed. Thanks Brian Ripley for
+ pointing this out.
+
+
Version: 0.7.8 [2006-05-22]
-o Added the TextStatusBar class.
-
+ o Added the TextStatusBar class.
+
+
Version: 0.7.7 [2006-03-30]
-o The method list in the class-overview help page was missing
- for several classes.
-o Added as.double() to Verbose.
-o saveAnywhere() of Settings now returns (invisibly) the pathname
- where the settings were saved.
+ o The method list in the class-overview help page was missing
+ for several classes.
-Version: 0.7.6 [2006-02-15]
-o Since the png2() and jpeg2() devices are in this package, the eps()
- device from R.graphics has been moved here for consistency.
+ o Added as.double() to Verbose.
+ o saveAnywhere() of Settings now returns (invisibly) the pathname
+ where the settings were saved.
+
+
+Version: 0.7.6 [2006-02-15]
+ o Since the png2() and jpeg2() devices are in this package, the eps()
+ device from R.graphics has been moved here for consistency.
+
+
Version: 0.7.5 [2006-02-09]
-o as.character.hexmode() is available in R v2.3.0 and forward. Thus,
- the method is only added by this package for pre-R v2.3.0.
-
+ o as.character.hexmode() is available in R v2.3.0 and forward. Thus,
+ the method is only added by this package for pre-R v2.3.0.
+
+
Version: 0.7.4 [2005-12-23]
-o Updated getHostname() and getUsername() in System to first try to
- find the details using Sys.info(). After that system environment
- variable and so on are checked.
-o Added argument 'expandTilde=FALSE' to getAbsolutePath() so
- that tildes (~) are expanded to there corresponding path.
-o Now relative paths handle tildes too.
-o Added optional automatic timestamping for the Verbose class.
- This is useful for Verbose objects writing to log files.
-o BUG FIX: Added protection against infinite loops in isFile(),
- where relative path is the same as the absolute path.
+ o Updated getHostname() and getUsername() in System to first try to
+ find the details using Sys.info(). After that system environment
+ variable and so on are checked.
-Version: 0.7.3 [2005-11-24]
-o Added extract() for arrays, amtrices and vectors.
+ o Added argument 'expandTilde = FALSE' to getAbsolutePath() so
+ that tildes (~) are expanded to there corresponding path.
+
+ o Now relative paths handle tildes too.
+
+ o Added optional automatic timestamping for the Verbose class.
+ This is useful for Verbose objects writing to log files.
+ o BUG FIX: Added protection against infinite loops in isFile(),
+ where relative path is the same as the absolute path.
+
+
+Version: 0.7.3 [2005-11-24]
+ o Added extract() for arrays, amtrices and vectors.
+
+
Version: 0.7.2 [2005-11-22]
-o BUG FIX: filePath(..., expandLinks="any") would return the relative
- link instead of the network pathname, even if there were no local
- pathname.
-o BUG FIX: Now using scan() instead of readLines() to parse header.
- This way the header can now also be quoted.
-o BUG FIX: Missing object 'ndim' in wrap(); should be 'ndims'.
-o BUG FIX: Sequences of length one was given as intervals by
- seqToHumanReadable(), e.g. 10-10.
-o Static Arguments class: Added getReadablePathnames(). Now getCharacter()
- accepts vectors of length zero or one only.
+ o BUG FIX: filePath(..., expandLinks = "any") would return the relative
+ link instead of the network pathname, even if there were no local
+ pathname.
-Version: 0.7.1 [2005-11-12]
-o Added functions wrap() and unwrap() to reshape arrays (and matrices)
- by joining and splitting dimensions, respectively, and optionally
- by permuting dimensions too. This is for instance useful when storing
- multidimensional arrays in tabular formats.
+ o BUG FIX: Now using scan() instead of readLines() to parse header.
+ This way the header can now also be quoted.
+
+ o BUG FIX: Missing object 'ndim' in wrap(); should be 'ndims'.
+ o BUG FIX: Sequences of length one was given as intervals by
+ seqToHumanReadable(), e.g. 10-10.
+ o Static Arguments class: Added getReadablePathnames(). Now getCharacter()
+ accepts vectors of length zero or one only.
+
+
+Version: 0.7.1 [2005-11-12]
+
+ o Added functions wrap() and unwrap() to reshape arrays (and matrices)
+ by joining and splitting dimensions, respectively, and optionally
+ by permuting dimensions too. This is for instance useful when storing
+ multidimensional arrays in tabular formats.
+
+
Version: 0.7.0 [2005-11-10]
-o Added trial version of readTable(). It extends the read.table()
- in two major ways. First it allows you to specify colClasses as
- a column name to column class map. Second, it allows you you to
- read any subset of rows, which substantially improves speed and
- decrease memory usage. Use readTableIndex() to create a look-up
- index for rows of interest.
-o Added seqToIntervals(), which finds all contigous (integer) regions
- in a set of integers, cf. seqToHumanReadable().
-o BUG FIX: isDirectory() on a file would result in an infinite recursive
- loop to itself.
-o Added inifite recursive call detection to listDirectory().
-o Now sourceDirectory() returns the source files invisibly.
-o Gathered files recursively in sourceDirectory(), but it was not needed
- since sourceDirectory() itself is recursive.
+ o Added trial version of readTable(). It extends the read.table()
+ in two major ways. First it allows you to specify colClasses as
+ a column name to column class map. Second, it allows you you to
+ read any subset of rows, which substantially improves speed and
+ decrease memory usage. Use readTableIndex() to create a look-up
+ index for rows of interest.
-Version: 0.6.3 [2005-10-26]
-o Renamed argument 'overwrite' in getWritablePathname() in Arguments to
- 'mustNotExist'. Renamed all 'mustExists' to 'mustExist' in all methods
- of class Arguments.
+ o Added seqToIntervals(), which finds all contigous (integer) regions
+ in a set of integers, cf. seqToHumanReadable().
+ o BUG FIX: isDirectory() on a file would result in an infinite recursive
+ loop to itself.
+ o Added inifite recursive call detection to listDirectory().
+
+ o Now sourceDirectory() returns the source files invisibly.
+
+ o Gathered files recursively in sourceDirectory(), but it was not needed
+ since sourceDirectory() itself is recursive.
+
+
+Version: 0.6.3 [2005-10-26]
+
+ o Renamed argument 'overwrite' in getWritablePathname() in Arguments to
+ 'mustNotExist'. Renamed all 'mustExists' to 'mustExist' in all methods
+ of class Arguments.
+
+
Version: 0.6.2 [2005-10-20]
-o Update loadAnywhere() for the Settings clas so that it works on
- objects too for which the default basename is the static basename.
-o BUG FIX: getLeaves() would give an error for empty Options objects.
-o BUG FIX: filePath(".") would return "".
-o BUG FIX: filePath("//shared/foo") would return "/shared/foo".
+ o Update loadAnywhere() for the Settings clas so that it works on
+ objects too for which the default basename is the static basename.
-Version: 0.6.1 [2005-10-17]
-o BUG FIX: readWindowsShortcut() failed on some Network-only links.
+ o BUG FIX: getLeaves() would give an error for empty Options objects.
+ o BUG FIX: filePath(".") would return "".
+ o BUG FIX: filePath("//shared/foo") would return "/shared/foo".
+
+
+Version: 0.6.1 [2005-10-17]
+
+ o BUG FIX: readWindowsShortcut() failed on some Network-only links.
+
+
Version: 0.6.0 [2005-09-24]
-o Now filePath() removes repeated '/' and '\\', except for network
- files such as \\server\foo\bar.
-o BUG FIX: Argument 'pager' of displayCode() did not support functions.
-o Updated Options class to make it easier for subclasses to retrieve
- options more easy. This was needed for the future ROptions class
- to map to options().
-o BUG FIX: System$openBrowser() was broken, because startsWith() and
- endsWith() were missing.
-o Added trial version of jpeg2() and png2().
+ o Now filePath() removes repeated '/' and '\\', except for network
+ files such as \\server\foo\bar.
-Version: 0.5.9 [2005-09-18]
-o Added static function findGraphicsDevice() to System. The methods
- search for a working device among a list of potential ones. This
- is for instance useful if it is known in advance that the PNG
- device is available (then the bitmap() device is an option).
+ o BUG FIX: Argument 'pager' of displayCode() did not support functions.
+ o Updated Options class to make it easier for subclasses to retrieve
+ options more easy. This was needed for the future ROptions class
+ to map to options().
+ o BUG FIX: System$openBrowser() was broken, because startsWith() and
+ endsWith() were missing.
+
+ o Added trial version of jpeg2() and png2().
+
+
+Version: 0.5.9 [2005-09-18]
+
+ o Added static function findGraphicsDevice() to System. The methods
+ search for a working device among a list of potential ones. This
+ is for instance useful if it is known in advance that the PNG
+ device is available (then the bitmap() device is an option).
+
+
Version: 0.5.8 [2005-09-06]
-o Added argument asGString=TRUE to the Verbose constructor.
-o Added remove() to FileProgressBar.
-o Replace argument 'gString' of getCharacters() to 'asGString', cf.
- Verbose class.
-o Now Arguments$getReadablePathname() follows Windows shortcut files.
-o BUG FIX: displayCode() was interpreting the code as GString:s.
-o Now making use of relative pathnames internally in copyDirectory().
- Sometimes relative pathnames will work when the absolute ones does
- not (because of missing file access rights).
-o BUG FIX: copyDirectory() would not return copied files if recursive==TRUE.
-o BUG FIX: Smart comments preceeded by TABs would not be recognized.
-o GString's parse() could return warning because it was incorrectly
- assumed that regexpr() did not return more than one value.
+ o Added argument asGString = TRUE to the Verbose constructor.
-Version: 0.5.7 [2005-08-12]
-o Function filePath() returns NULL, if no arguments or only NULL
- arguments are passed to it.
+ o Added remove() to FileProgressBar.
+
+ o Replace argument 'gString' of getCharacters() to 'asGString', cf.
+ Verbose class.
+
+ o Now Arguments$getReadablePathname() follows Windows shortcut files.
+ o BUG FIX: displayCode() was interpreting the code as GString:s.
+ o Now making use of relative pathnames internally in copyDirectory().
+ Sometimes relative pathnames will work when the absolute ones does
+ not (because of missing file access rights).
+
+ o BUG FIX: copyDirectory() would not return copied files if recursive == TRUE.
+
+ o BUG FIX: Smart comments preceeded by TABs would not be recognized.
+
+ o GString's parse() could return warning because it was incorrectly
+ assumed that regexpr() did not return more than one value.
+
+
+Version: 0.5.7 [2005-08-12]
+
+ o Function filePath() returns NULL, if no arguments or only NULL
+ arguments are passed to it.
+
+
Version: 0.5.6 [2005-08-02]
-o BUG FIX: splitByPattern() tried to access non-existing class Argument.
-o Arguments' getReadablePathname() no longer returns the absolute pathname
- by default. This is because on some systems the relative pathname can
- be queried wheras the absolute one may not be access due to missing
- file permissions.
-o isFile() and isDirectory() is now comparing to current working directory
- if no file information is available (due to missing file permissions);
- assumes that the current working directory always exists.
-o getParent() now returns NULL instead of "".
-o Added argument 'caseSensitive' to getRelativePath().
-o isAbsolutePath(NULL) returns FALSE.
-o mkdirs() tries to create directory with relative path if absolute
- path fails. This sometimes works when the file permission are missing.
-o Added argument 'code' to displayCode(). The function now also used
- file.show() to display the code.
-o Added isUrl() and hasUrlProtocol().
-o Added copyDirectory().
-o Added getEnvironment() and getRegularExpression() to Arguments.
+ o BUG FIX: splitByPattern() tried to access non-existing class Argument.
+
+ o Arguments' getReadablePathname() no longer returns the absolute pathname
+ by default. This is because on some systems the relative pathname can
+ be queried wheras the absolute one may not be access due to missing
+ file permissions.
+ o isFile() and isDirectory() is now comparing to current working directory
+ if no file information is available (due to missing file permissions);
+ assumes that the current working directory always exists.
+
+ o getParent() now returns NULL instead of "".
+
+ o Added argument 'caseSensitive' to getRelativePath().
+
+ o isAbsolutePath(NULL) returns FALSE.
+
+ o mkdirs() tries to create directory with relative path if absolute
+ path fails. This sometimes works when the file permission are missing.
+
+ o Added argument 'code' to displayCode(). The function now also used
+ file.show() to display the code.
+
+ o Added isUrl() and hasUrlProtocol().
+
+ o Added copyDirectory().
+
+ o Added getEnvironment() and getRegularExpression() to Arguments.
+
+
Version: 0.5.5 [2005-07-21]
-o BUG FIX: Example illustrating Windows Shortcut methods tried to
- access 'HISTORY.lnk' and not 'HISTORY.LNK', which would fail on Unix.
-o BUG FIX: getCharacters() would not coerce Object:s correctly.
-o Now sourceDirectory() does 'chdir=FALSE' instead of 'chdir=FALSE'.
-o Now mkdirs() has an internal check for infinit-recursive calls.
+ o BUG FIX: Example illustrating Windows Shortcut methods tried to
+ access 'HISTORY.lnk' and not 'HISTORY.LNK', which would fail on Unix.
+
+ o BUG FIX: getCharacters() would not coerce Object:s correctly.
+ o Now sourceDirectory() does 'chdir = FALSE' instead of 'chdir = FALSE'.
+
+ o Now mkdirs() has an internal check for infinit-recursive calls.
+
+
Version: 0.5.4 [2005-07-19]
-o BUG FIX: If there are no files to source in a directory, and verbose
- is active, basefile() on NULL was called generating an error.
-o BUG FIX: sourceTo(..., chdir=TRUE) would generate an error. This
- would for instance make sourceDirectory() useless.
+ o BUG FIX: If there are no files to source in a directory, and verbose
+ is active, basefile() on NULL was called generating an error.
+ o BUG FIX: sourceTo(..., chdir = TRUE) would generate an error. This
+ would for instance make sourceDirectory() useless.
+
+
Version: 0.5.3 [2005-07-18]
-o Added resetWarnings() and splitByPattern().
-o Added summary() to class Verbose and a corresponding VComments tag.
-o Arguments$getCharacters() returned attribute 'names' too. Removed.
-o sourceDirectory() is no longer catching warnings in tryCatch(),
- because otherwise it will interrupt the call as if the warnings
- were errors.
+ o Added resetWarnings() and splitByPattern().
+
+ o Added summary() to class Verbose and a corresponding VComments tag.
+
+ o Arguments$getCharacters() returned attribute 'names' too. Removed.
+ o sourceDirectory() is no longer catching warnings in tryCatch(),
+ because otherwise it will interrupt the call as if the warnings
+ were errors.
+
+
Version: 0.5.2 [2005-06-27]
-o Added getRelativePath().
-o Added LComments which is a VComments class with different defaults.
-o Made SmartComments classes and methods non-static.
-o Escaping double quotes in VComments messages.
+ o Added getRelativePath().
+ o Added LComments which is a VComments class with different defaults.
+
+ o Made SmartComments classes and methods non-static.
+
+ o Escaping double quotes in VComments messages.
+
+
Version: 0.5.1 [2005-06-23]
-o Package passes R CMD check for R v2.1.0.
-o Added trial version of SmartComments and subclass VComments where
- the latter are R comments with a special format generating verbose
- output if source is first pre-processed by compile() method.
- If not preprocessed, they are just regular comments, adding no
- overhead in processing speed. I can imagine to add, say, AComments
- that Asserts conditions at given test points in code; when code
- works, just source code without pre-processing them!
-o Now it is possible to set the default verbose level used by
- all Verbose methods if not explicitly given.
-o Now all Verbose messages are GString:ed. This makes VComments slim.
+ o Package passes R CMD check for R v2.1.0.
+
+ o Added trial version of SmartComments and subclass VComments where
+ the latter are R comments with a special format generating verbose
+ output if source is first pre-processed by compile() method.
+ If not preprocessed, they are just regular comments, adding no
+ overhead in processing speed. I can imagine to add, say, AComments
+ that Asserts conditions at given test points in code; when code
+ works, just source code without pre-processing them!
+ o Now it is possible to set the default verbose level used by
+ all Verbose methods if not explicitly given.
+
+ o Now all Verbose messages are GString:ed. This makes VComments slim.
+
+
Version: 0.5.0 [2005-06-19]
-o Package passes R CMD check for R v2.1.0.
-o Now commandArgs() recognizes environment variables.
-o Added attachLocally().
-o When package is loaded, .Last() is modified so that 'onSessionExit'
- hooks are called when R finishes.
-o Added onSessionExit(), finalizeSession() and addFinalizerToLast().
-o Added callHooks().
-o Added the NullVerbose() class.
-o Moved (de-)capitalize() and seqToHumanReadable() from R.basic to here.
-o Added new GString class.
-o Added the Assert class.
-o Moved the System class from R.lang to this package. System was also
- cleaned out from several never used methods and fields.
-o Added filePath() together with file methods isFile(), isDirectory(),
- isAbsolutePath(), mkdirs(), lastModified(), and toUrl().
-o Moved sourceTo() from R.io to this package.
-o Moved doCall() from R.basic to this package.
-o Created the Options class.
-o Added several methods to the Verbose class. Also added support for
- indentation by enter() and exit() of Verbose.
-o Moved the Java and Verbose class from R.matlab to this package.
- This requires that this package is on CRAN before R.matlab is updated.
-o Moved the ProgressBar and FileProgressBar from the R.ui package,
- which then becomes more or less empty.
-o Created.
+
+ o Package passes R CMD check for R v2.1.0.
+
+ o Now commandArgs() recognizes environment variables.
+
+ o Added attachLocally().
+
+ o When package is loaded, .Last() is modified so that 'onSessionExit'
+ hooks are called when R finishes.
+
+ o Added onSessionExit(), finalizeSession() and addFinalizerToLast().
+
+ o Added callHooks().
+
+ o Added the NullVerbose() class.
+
+ o Moved (de-)capitalize() and seqToHumanReadable() from R.basic to here.
+
+ o Added new GString class.
+
+ o Added the Assert class.
+
+ o Moved the System class from R.lang to this package. System was also
+ cleaned out from several never used methods and fields.
+
+ o Added filePath() together with file methods isFile(), isDirectory(),
+ isAbsolutePath(), mkdirs(), lastModified(), and toUrl().
+
+ o Moved sourceTo() from R.io to this package.
+
+ o Moved doCall() from R.basic to this package.
+
+ o Created the Options class.
+
+ o Added several methods to the Verbose class. Also added support for
+ indentation by enter() and exit() of Verbose.
+
+ o Moved the Java and Verbose class from R.matlab to this package.
+ This requires that this package is on CRAN before R.matlab is updated.
+
+ o Moved the ProgressBar and FileProgressBar from the R.ui package,
+ which then becomes more or less empty.
+
+ o Created.
diff --git a/R/compressFile.R b/R/compressFile.R
index 18e0e9e..bb79a7a 100755
--- a/R/compressFile.R
+++ b/R/compressFile.R
@@ -69,7 +69,11 @@
# Returns the pathname of the output file.
# The number of bytes processed is returned as an attribute.
#
-# \code{isCompressedFile()} etc. return a @logical.
+# \code{isCompressedFile()}, \code{isGzipped()} and \code{isBzipped()}
+# return a @logical.
+# Note that with \code{method = "extension"} (default), only the filename
+# extension is used to infer whether the file is compressed or not.
+# Specifically, it does not matter whether the file actually exists or not.
# }
#
# \details{
diff --git a/R/fileAccess.R b/R/fileAccess.R
index 88d8de0..1460d47 100644
--- a/R/fileAccess.R
+++ b/R/fileAccess.R
@@ -43,7 +43,8 @@
# \references{
# [1] R-devel thread
# \emph{file.access() on network (mounted) drive on Windows Vista?}
-# on Nov 26, 2008.\cr
+# on Nov 26, 2008.
+# \url{https://stat.ethz.ch/pipermail/r-devel/2008-December/051461.html}\cr
# [2] Filesystem permissions, Wikipedia, 2010.
# \url{http://en.wikipedia.org/wiki/Filesystem_permissions}\cr
# }
diff --git a/R/findSourceTraceback.R b/R/findSourceTraceback.R
index db39595..fa9bbbc 100644
--- a/R/findSourceTraceback.R
+++ b/R/findSourceTraceback.R
@@ -1 +1 @@
-###########################################################################/**
# @RdocDefault findSourceTraceback
#
# @title "Finds all 'srcfile' objects generated by source() in all call frames"
#
# @synopsis
#
# \description{
# @get "title". This makes it possible to find out which files are
# currently scripted by @see "base::source".
# }
#
# \arguments{
# \item{...}{Not used.}
# }
#
# \value{
# Returns a named list of @see "base::srcfile" objects and/or
# @character strings.
# The names of the list entries corresponds to the 'filename'
# value of each corresponding 'srcfile' object.
# The returned list is empty if @see "base::source" was not called.
# }
#
# @examples "../incl/findSourceTraceback.Rex"
#
# @author
#
# \seealso{
# See also @see "utils::sourceutils".
# }
#
# @keyword IO
# @keyword programming
#*/###########################################################################
setMethodS3("findSourceTraceback", "default", function(...) {
# Identify the environment/frame of interest by making sure
# it at least contains all the arguments of source().
argsToFind <- names(formals(source));
# Scan the call frames/environments backwards...
srcfileList <- list();
for (ff in sys.nframe():0) {
env <- sys.frame(ff);
# Does the environment look like a source() environment?
exist <- sapply(argsToFind, FUN=exists, envir=env, inherits=FALSE);
if (!all(exist)) {
# Nope, then skip to the next one
next;
}
# Identify the source file
srcfile <- get("srcfile", envir=env, inherits=FALSE);
if (!is.null(srcfile)) {
if (!is.function(srcfile)) {
srcfileList <- c(srcfileList, list(srcfile));
}
}
} # for (ff ...)
# Extract the pathnames to the files called
pathnames <- sapply(srcfileList, FUN=function(srcfile) {
if (inherits(srcfile, "srcfile")) {
pathname <- srcfile$filename;
} else if (is.environment(srcfile)) {
pathname <- srcfile$filename;
} else if (is.character(srcfile)) {
# Occurs with source(..., keep.source=FALSE)
pathname <- srcfile;
} else {
pathname <- NA_character_;
warning("Unknown class of 'srcfile': ", class(srcfile)[1L]);
}
pathname;
});
names(srcfileList) <- pathnames;
srcfileList;
}) # findSourceTraceback()
############################################################################
# HISTORY:
# 2013-07-27
# o BUG FIX: findSourceTraceback() would give an error "Unknown class of
# 'srcfile': character" for source(..., keep.source=FALSE) in recent
# R devel and R v3.0.1 patched. Thanks Duncan Murdoch for the report.
# 2012-06-07
# o DOCUMENTATION: Added a link to help("sourceutils", package="utils").
# 2010-09-29
# o BUG FIX: Each entry identified by findSourceTraceback() would
# be duplicated.
# o Added an example to help(findSourceTraceback).
# 2010-03-02
# o BUG FIX: findSourceTraceback() stopped working; probably due to some
# recent updates in base::source().
# 2009-10-20
# o Created.
############################################################################
\ No newline at end of file
+###########################################################################/**
# @RdocDefault findSourceTraceback
#
# @title "Finds all 'srcfile' objects generated by source() in all call frames"
#
# @synopsis
#
# \description{
# @get "title". This makes it possible to find out which files are
# currently scripted by @see "base::source".
# }
#
# \arguments{
# \item{...}{Not used.}
# }
#
# \value{
# Returns a named list of @see "base::srcfile" objects and/or
# @character strings.
# The names of the list entries corresponds to the 'filename'
# value of each corresponding 'srcfile' object.
# The returned list is empty if @see "base::source" was not called.
# }
#
# @examples "../incl/findSourceTraceback.Rex"
#
# @author
#
# \seealso{
# See also @see "utils::sourceutils".
# }
#
# @keyword IO
# @keyword programming
#*/###########################################################################
setMethodS3("findSourceTraceback", "default", function(...) {
# Identify the environment/frame of interest by making sure
# it at least contains all the arguments of source().
argsToFind <- names(formals(base::source));
# Scan the call frames/environments backwards...
srcfileList <- list();
for (ff in sys.nframe():0) {
env <- sys.frame(ff);
# Does the environment look like a source() environment?
exist <- sapply(argsToFind, FUN=exists, envir=env, inherits=FALSE);
if (!all(exist)) {
# Nope, then skip to the next one
next;
}
# Identity the source file
if (exists("srcfile", envir=env, inherits=FALSE)) {
srcfile <- get("srcfile", envir=env, inherits=FALSE)
} else {
## AD HOC: Needed when for instance 'XML' is attached
srcfile <- get("srcfile", envir=env, inherits=TRUE)
## Failed?
if (!inherits(srcfile, "srcfile")) srcfile <- NULL
}
if (!is.null(srcfile)) {
if (!is.function(srcfile)) {
srcfileList <- c(srcfileList, list(srcfile));
}
}
} # for (ff ...)
# Extract the pathnames to the files called
pathnames <- sapply(srcfileList, FUN=function(srcfile) {
if (inherits(srcfile, "srcfile")) {
pathname <- srcfile$filename;
} else if (is.environment(srcfile)) {
pathname <- srcfile$filename;
} else if (is.character(srcfile)) {
# Occurs with source(..., keep.source=FALSE)
pathname <- srcfile;
} else {
pathname <- NA_character_;
warning("Unknown class of 'srcfile': ", class(srcfile)[1L]);
}
pathname;
});
names(srcfileList) <- pathnames;
srcfileList;
}) # findSourceTraceback()
############################################################################
# HISTORY:
# 2013-07-27
# o BUG FIX: findSourceTraceback() would give an error "Unknown class of
# 'srcfile': character" for source(..., keep.source=FALSE) in recent
# R devel and R v3.0.1 patched. Thanks Duncan Murdoch for the report.
# 2012-06-07
# o DOCUMENTATION: Added a link to help("sourceutils", package="utils").
# 2010-09-29
# o BUG FIX: Each entry identified by findSourceTraceback() would
# be duplicated.
# o Added an example to help(findSourceTraceback).
# 2010-03-02
# o BUG FIX: findSourceTraceback() stopped working; probably due to some
# recent updates in base::source().
# 2009-10-20
# o Created.
############################################################################
\ No newline at end of file
diff --git a/R/gcDLLs.R b/R/gcDLLs.R
index 8c596ee..40de05b 100644
--- a/R/gcDLLs.R
+++ b/R/gcDLLs.R
@@ -16,6 +16,7 @@
# @synopsis
#
# \arguments{
+# \item{gc}{If @TRUE, if there are stray DLLs, then the garbage collector is run before unloading those DLLs. This is done in order to trigger any finalizers, of which some may need those DLLs, to be called.}
# \item{quiet}{If @FALSE, a message is outputted for every stray DLL that is unloaded.}
# }
#
@@ -32,6 +33,11 @@
# following to your package:
# \preformatted{
# .onUnload <- function(libpath) {
+# ## (1) Force finalizers to be called before removing the DLL
+# ## in case some of them need the DLL.
+# gc()
+#
+# ## (2) Unload the DLL for this package
# library.dynam.unload(.packageName, libpath)
# }
# }
@@ -81,9 +87,18 @@ strayDLLs <- function() {
} ## strayDLLs()
-gcDLLs <- function(quiet = TRUE) {
+gcDLLs <- function(gc = TRUE, quiet = TRUE) {
## Find all package DLLs for which no package is loaded
dlls <- strayDLLs()
+
+ ## Nothing to do?
+ if (length(dlls) == 0) return(dlls)
+
+ ## Garbage collect to trigger finalizers that may still use some
+ ## of these DLLs? See Karl Miller's comments in R-devel thread
+ ## 'Request: Increasing MAX_NUM_DLLS in Rdynload.c' on 2016-12-20
+ ## https://stat.ethz.ch/pipermail/r-devel/2016-December/073537.html
+ if (gc) gc(verbose = !quiet)
## Unload DLLs
for (dll in dlls) {
diff --git a/R/intToBin.R b/R/intToBin.R
deleted file mode 100755
index 178ede9..0000000
--- a/R/intToBin.R
+++ /dev/null
@@ -1,103 +0,0 @@
-########################################################################/**
-# @RdocFunction as.character.binmode
-#
-# @title "Converts a binary/octal/hexadecimal number into a string"
-#
-# \description{
-# @get "title".
-# }
-#
-# \usage{
-# @usage as.character,binmode
-# }
-#
-# \arguments{
-# \item{x}{Object to be converted.}
-# \item{...}{Not used.}
-# }
-#
-# \value{
-# Returns a @character.
-# }
-#
-# @author
-#
-# \seealso{
-# \code{as.character.octmode()}, cf. @see "base::octmode".
-# @see "intToBin" (incl. \code{intToOct()} and \code{intToHex()}).
-# }
-#
-# @keyword manip
-# @keyword character
-# @keyword programming
-#*/########################################################################
-setMethodS3("as.character", "binmode", function(x, ...) {
- isna <- is.na(x);
- y <- x[!isna];
- ans0 <- character(length(y));
- z <- NULL;
- while (any(y > 0) | is.null(z)) {
- z <- y%%2;
- y <- floor(y/2);
- ans0 <- paste(z, ans0, sep = "");
- }
- ans <- rep(as.character(NA), length(x));
- ans[!isna] <- ans0;
- ans;
-})
-
-
-
-
-########################################################################/**
-# @RdocFunction intToBin
-# @alias intToOct
-# @alias intToHex
-#
-# @title "Converts an integer to a binary/octal/hexadecimal number"
-#
-# \description{
-# @get "title".
-# }
-#
-# \usage{
-# intToBin(x)
-# intToOct(x)
-# intToHex(x)
-# }
-#
-# \arguments{
-# \item{x}{An @integer to be converted.}
-# }
-#
-# \value{
-# Returns a @character.
-# }
-#
-# @author
-#
-# @keyword manip
-# @keyword character
-# @keyword programming
-#*/########################################################################
-intToBin <- function(x) {
- y <- as.integer(x);
- class(y) <- "binmode";
- y <- as.character(y);
- dim(y) <- dim(x);
- y;
-}
-
-
-############################################################################
-# HISTORY:
-# 2008-07-03
-# o Removed documentation for as.character() for 'hexmode' since it is
-# now in the 'base' package.
-# 2005-02-20
-# o Now using setMethodS3() and added '...' to please R CMD check.
-# 2004-10-18
-# o Added Rdoc comments.
-# 2002-07-18
-# o Created from intToOct.R.
-############################################################################
diff --git a/R/intToHex.R b/R/intToHex.R
index 25bfe3a..8383fd8 100755
--- a/R/intToHex.R
+++ b/R/intToHex.R
@@ -1,22 +1,129 @@
+########################################################################/**
+# @RdocFunction as.character.binmode
+#
+# @title "Converts a binary/octal/hexadecimal number into a string"
+#
+# \description{
+# @get "title".
+# }
+#
+# \usage{
+# @usage as.character,binmode
+# }
+#
+# \arguments{
+# \item{x}{Object to be converted.}
+# \item{...}{Not used.}
+# }
+#
+# \value{
+# Returns a @character.
+# }
+#
+# @author
+#
+# \seealso{
+# \code{as.character.octmode()}, cf. @see "base::octmode".
+# @see "intToBin" (incl. \code{intToOct()} and \code{intToHex()}).
+# }
+#
+# @keyword manip
+# @keyword character
+# @keyword programming
+#*/########################################################################
+setMethodS3("as.character", "binmode", function(x, ...) {
+ isna <- is.na(x)
+ y <- x[!isna]
+ ans0 <- character(length = length(y))
+
+ ## Handle negative values specially; emulates octmode and hexmode
+ neg <- which(y < 0)
+ if (length(neg) > 0) {
+ y[neg] <- y[neg] + 1L + .Machine$integer.max
+ }
+
+ z <- NULL
+ while (any(y > 0) || is.null(z)) {
+ z <- y %% 2
+ y <- floor(y / 2)
+ ans0 <- paste(z, ans0, sep = "")
+ }
+
+ ans <- rep(NA_character_, times = length(x))
+ ans[!isna] <- ans0
+ ans
+})
+
+
+
+
+########################################################################/**
+# @RdocFunction intToBin
+# @alias intToOct
+# @alias intToHex
+#
+# @title "Converts an integer to a binary/octal/hexadecimal number"
+#
+# \description{
+# @get "title".
+# }
+#
+# \usage{
+# intToBin(x)
+# intToOct(x)
+# intToHex(x)
+# }
+#
+# \arguments{
+# \item{x}{A @numeric vector of integers to be converted.}
+# }
+#
+# \value{
+# Returns a @character string of length \code{length(x)}.
+# For coercions out of range, \code{NA_character_} is returned for
+# such elements.
+# }
+#
+# \details{
+# For \code{length(x)} > 1, the number of characters in each of returned
+# elements is the same and driven by the \code{x} element that requires
+# the highest number of character - all other elements are padded with
+# zeros (or ones for negative values). This is why we for instance get
+# \code{intToHex(15) == "f"} but \code{intToHex(15:16) == c("0f", "10")}.
+#
+# The supported range for \code{intToHex()}, \code{intToOct()}, and
+# \code{intToBin()} is that of \R integers, i.e.
+# \code{[-.Machine$integer.max, +.Machine$integer.max]} where.
+# \code{.Machine$integer.max} is \eqn{2^31-1}.
+# This limitation is there such that negative values can be converted too.
+# }
+#
+# @author
+#
+# @keyword manip
+# @keyword character
+# @keyword programming
+#*/########################################################################
+intToBin <- function(x) {
+ y <- as.integer(x)
+ class(y) <- "binmode"
+ y <- as.character(y)
+ dim(y) <- dim(x)
+ y
+}
+
intToHex <- function(x) {
- y <- as.integer(x);
- class(y) <- "hexmode";
- y <- as.character(y);
- dim(y) <- dim(x);
- y;
+ y <- as.integer(x)
+ class(y) <- "hexmode"
+ y <- as.character(y)
+ dim(y) <- dim(x)
+ y
}
-############################################################################
-# HISTORY:
-# 2006-02-09
-# o as.character.hexmode() is available in R v2.3.0 and forward. Thus,
-# the method is only added by this package for pre-R v2.3.0.
-# 2005-02-20
-# o Now using setMethodS3() and added '...' to please R CMD check.
-# 2002-07-08
-# * BUG FIX: intToHex(0) gave "". Problem was in as.character.hexmode().
-# 2002-05-31
-# * intToX() now returns the result with same dimensions as the input.
-# 2002-04-13
-# * Created from intToOct() and as.character.octmode().
-############################################################################
+intToOct <- function(x) {
+ y <- as.integer(x)
+ class(y) <- "octmode"
+ y <- as.character(y)
+ dim(y) <- dim(x)
+ y
+}
diff --git a/R/intToOct.R b/R/intToOct.R
deleted file mode 100755
index 04ee888..0000000
--- a/R/intToOct.R
+++ /dev/null
@@ -1,22 +0,0 @@
-intToOct <- function(x) {
- y <- as.integer(x);
- class(y) <- "octmode";
- y <- as.character(y);
- dim(y) <- dim(x);
- y;
-}
-
-############################################################################
-# HISTORY:
-# 2004-10-18
-# o Removed as.character.octmode(), because it already exists in R.
-# 2002-07-18
-# o Removed the class check in as.character.octmode() because it is useful
-# to be able to call it anyway.
-# 2002-07-08
-# o BUG FIX: intToOct(0) gave "". Problem was in as.character.octmode().
-# 2002-05-31
-# o intToX() now returns the result with same dimensions as the input.
-# 2002-04-07
-# o Created.
-############################################################################
diff --git a/R/isEof.connection.R b/R/isEof.connection.R
index 10e1436..1e7bc86 100644
--- a/R/isEof.connection.R
+++ b/R/isEof.connection.R
@@ -19,6 +19,13 @@
# Returns a @logical.
# }
#
+# \details{
+# Internally @see base::seek is used, which according to to the \R help
+# is discouraged on Windows. However, after many years of large-scale
+# testing on various Windows versions and file systems we have yet to
+# experience issues with using \code{seek()} on Windows.
+# }
+#
# @author
#
# \seealso{
diff --git a/R/isSingle.R b/R/isSingle.R
index 4854278..6c0c1aa 100644
--- a/R/isSingle.R
+++ b/R/isSingle.R
@@ -2,7 +2,7 @@
# @RdocFunction isSingle
# @alias singles
#
-# @title "Identifies all entries that exists exactly ones"
+# @title "Identifies all entries that exists exactly once"
#
# \description{
# @get "title".
diff --git a/R/loadObject.R b/R/loadObject.R
index c66fe3f..ca945fe 100644
--- a/R/loadObject.R
+++ b/R/loadObject.R
@@ -64,14 +64,24 @@ setMethodS3("loadObject", "default", function(file, path=NULL, format=c("auto",
saveLoadReference <- NULL
# load.default() recognized gzip'ed files too.
- vars <- base::load(file=file)
+ tryCatch({
+ vars <- base::load(file = file)
+ }, error = function(ex) {
+ throw(sprintf("Failed to load file %s. The reason was: %s",
+ sQuote(file), conditionMessage(ex)))
+ })
if (!"saveLoadReference" %in% vars)
throw("The file was not saved by saveObject(): ", file)
res <- saveLoadReference
} else if (format == "rds") {
- res <- readRDS(file)
+ tryCatch({
+ res <- readRDS(file)
+ }, error = function(ex) {
+ throw(sprintf("Failed to load file %s. The reason was: %s",
+ sQuote(file), conditionMessage(ex)))
+ })
}
res
diff --git a/R/loadToEnv.R b/R/loadToEnv.R
index 4ec92d0..b01f0f9 100644
--- a/R/loadToEnv.R
+++ b/R/loadToEnv.R
@@ -28,9 +28,19 @@
# @keyword IO
# @keyword internal
#*/###########################################################################
-setMethodS3("loadToEnv", "default", function(..., envir=new.env()) {
- base::load(..., envir=envir);
- envir;
+setMethodS3("loadToEnv", "default", function(file, ..., envir = new.env()) {
+ tryCatch({
+ base::load(file = file, envir = envir, ...)
+ }, error = function(ex) {
+ if (is.character(file)) {
+ msg <- sprintf("Failed to load file %s.", sQuote(file))
+ } else {
+ msg <- sprintf("Failed to load from %s.", sQuote(class(file)[1]))
+ }
+ msg <- sprintf("%s The reason was: %s", msg, conditionMessage(ex))
+ throw(msg)
+ })
+ envir
}, private=TRUE) # loadToEnv()
diff --git a/R/nullfile.R b/R/nullfile.R
index 6c8344f..8274508 100644
--- a/R/nullfile.R
+++ b/R/nullfile.R
@@ -4,7 +4,7 @@
# @title "Gets the pathname of the NULL device on the current platform"
#
# \description{
-# @get "title". On Windows, it returns \code{"NIL"}. On all other
+# @get "title". On Windows, it returns \code{"NUL"}. On all other
# platforms include Unix and macOS it returns \code{"/dev/null"}.
# }
#
diff --git a/R/reassignInPackage.R b/R/reassignInPackage.R
index 94cd107..d95859f 100644
--- a/R/reassignInPackage.R
+++ b/R/reassignInPackage.R
@@ -13,8 +13,8 @@
# \item{name}{The name of the object to be replaced."}
# \item{pkgName}{The name of the package where the object lives."}
# \item{value}{The new value to be assigned.}
-# \item{keepOld}{If @TRUE, the old value is kept as an attribute in
-# the new object.}
+# \item{keepOld}{If @TRUE, the old value is kept as attribute
+# \code{oldValue} in the new object.}
# \item{...}{Not used.}
# }
#
diff --git a/R/shell.exec2.R b/R/shell.exec2.R
index 9ec5b95..f9d4932 100644
--- a/R/shell.exec2.R
+++ b/R/shell.exec2.R
@@ -26,7 +26,7 @@
# (i) unmaps any mapped drive letters used in the pathname
# (e.g. 'X:/foo.bar.html' to 'C:/Users/Joe/bar.html'),
# (ii) and replaces any forward slashed with backward ones
-# (e.g. 'C:\\Users\\Joe\\bar.html' to 'C:/Users/Joe/bar.html').
+# (e.g. 'C:/Users/Joe/bar.html' to 'C:\\Users\\Joe\\bar.html').
# URLs are passed as is to \code{shell.exec()}.
#
# The reason for (i) is that some web browsers (e.g. Google Chrome)
diff --git a/R/use.R b/R/use.R
index 930ce27..96ba9f6 100644
--- a/R/use.R
+++ b/R/use.R
@@ -53,7 +53,7 @@
# @keyword utilities
# @keyword internal
#*/###########################################################################
-setMethodS3("use", "default", function(pkg="R.utils", version=NULL, how=c("attach", "load"), quietly=TRUE, warn.conflicts=!quietly, install=TRUE, repos=getOption("use/repos", c("[[current]]", "[[mainstream]]")), ..., verbose=FALSE) {
+setMethodS3("use", "default", function(pkg="R.utils", version=NULL, how=c("attach", "load"), quietly=TRUE, warn.conflicts=!quietly, install=getOption("R.utils.use.install", Sys.getenv("R_R_UTILS_USE_INSTALL", "TRUE")), repos=getOption("use/repos", c("[[current]]", "[[mainstream]]")), ..., verbose=FALSE) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Local functions
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -236,7 +236,7 @@ setMethodS3("use", "default", function(pkg="R.utils", version=NULL, how=c("attac
quietly <- Arguments$getLogical(quietly);
# Argument 'install':
- install <- Arguments$getLogical(install);
+ install <- Arguments$getLogical(install, coerce = TRUE)
# Argument 'verbose':
verbose <- Arguments$getVerbose(verbose);
diff --git a/R/withCapture.R b/R/withCapture.R
index 915a01d..15db349 100644
--- a/R/withCapture.R
+++ b/R/withCapture.R
@@ -12,7 +12,7 @@
#
# \arguments{
# \item{expr}{The R expression to be evaluated.}
-# \item{substitute}{An optional named @list used for substituting
+# \item{replace}{An optional named @list used for substituting
# symbols with other strings.}
# \item{code}{If @TRUE, the deparsed code of the expression is echoed.}
# \item{output}{If @TRUE, the output of each evaluated subexpression
@@ -26,6 +26,7 @@
# is appended at the end.}
# \item{collapse}{A @character string used for collapsing the captured
# rows. If @NULL, the rows are not collapsed.}
+# \item{substitute}{(to be deprecated) use \code{replace} instead.}
# \item{envir}{The @environment in which the expression is evaluated.}
# }
#
@@ -43,24 +44,30 @@
#
# @keyword utilities
#*/###########################################################################
-withCapture <- function(expr, substitute=getOption("withCapture/substitute", ".x."), code=TRUE, output=code, ..., max.deparse.length=getOption("max.deparse.length", 10e3), trim=TRUE, newline=getOption("withCapture/newline", TRUE), collapse="\n", envir=parent.frame()) {
+withCapture <- function(expr, replace=getOption("withCapture/substitute", ".x."), code=TRUE, output=code, ..., max.deparse.length=getOption("max.deparse.length", 10e3), trim=TRUE, newline=getOption("withCapture/newline", TRUE), collapse="\n", substitute=replace, envir=parent.frame()) {
# Get code/expression without evaluating it
expr2 <- substitute(expr);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Substitute?
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ## 'substitute' will become deprecated in favor of 'replace'.
+ if (!missing(substitute) && missing(replace)) {
+ .Deprecated(msg = "Argument 'substitute' of withCapture() has been renamed to 'replace'")
+ replace <- substitute
+ }
+
# (a) Substitute by "constant" symbols?
- if (is.list(substitute) && (length(substitute) > 0L)) {
- names <- names(substitute);
- if (is.null(names)) throw("Argument 'substitute' must be named.");
- expr2 <- do.call(base::substitute, args=list(expr2, substitute))
+ if (is.list(replace) && (length(replace) > 0L)) {
+ names <- names(replace);
+ if (is.null(names)) throw("Argument 'replace' must be named.");
+ expr2 <- do.call(base::substitute, args=list(expr2, replace))
}
- # (b) Substitute code by regular expressions?
- if (is.character(substitute) && (length(substitute) > 0L)) {
- patterns <- names(substitute);
- replacements <- substitute;
+ # (b) Replace code by regular expressions?
+ if (is.character(replace) && (length(replace) > 0L)) {
+ patterns <- names(replace);
+ replacements <- replace;
# Predefined rules?
if (is.null(patterns)) {
@@ -81,9 +88,9 @@ withCapture <- function(expr, substitute=getOption("withCapture/substitute", ".x
}
}
- if (is.null(patterns)) throw("Argument 'substitute' must be named.");
+ if (is.null(patterns)) throw("Argument 'replace' must be named.");
- # (b) Substitute via regular expression
+ # (b) Replace via regular expression
for (kk in seq_along(replacements)) {
pattern <- patterns[kk];
replacement <- replacements[kk];
diff --git a/R/withLocale.R b/R/withLocale.R
index 1bcd48d..3d74c72 100644
--- a/R/withLocale.R
+++ b/R/withLocale.R
@@ -15,6 +15,8 @@
# \item{locale}{@character @vector specifying the locale to used. The
# first successfully set one will be used.}
# \item{...}{Not used.}
+# \item{substitute}{If @TRUE, argument \code{expr} is
+# \code{\link[base]{substitute}()}:ed, otherwise not.}
# \item{envir}{The @environment in which the expression should be evaluated.}
# }
#
@@ -34,9 +36,9 @@
# @keyword IO
# @keyword programming
#*/###########################################################################
-withLocale <- function(expr, category, locale, ..., envir=parent.frame()) {
- # Argument '.expr':
- expr <- substitute(expr)
+withLocale <- function(expr, category, locale, ..., substitute=TRUE, envir=parent.frame()) {
+ # Argument 'expr':
+ if (substitute) expr <- substitute(expr)
# Argument 'envir':
if (!is.environment(envir)) {
diff --git a/R/withOptions.R b/R/withOptions.R
index ac7eeeb..dfc6710 100644
--- a/R/withOptions.R
+++ b/R/withOptions.R
@@ -13,6 +13,8 @@
# \item{expr}{The R expression to be evaluated.}
# \item{...}{Named options to be used.}
# \item{args}{(optional) Additional named options specified as a named @list.}
+# \item{substitute}{If @TRUE, argument \code{expr} is
+# \code{\link[base]{substitute}()}:ed, otherwise not.}
# \item{envir}{The @environment in which the expression should be evaluated.}
# }
#
@@ -39,9 +41,9 @@
# @keyword IO
# @keyword programming
#*/###########################################################################
-withOptions <- function(expr, ..., args=list(), envir=parent.frame()) {
- # Argument '.expr':
- expr <- substitute(expr)
+withOptions <- function(expr, ..., args=list(), substitute=TRUE, envir=parent.frame()) {
+ # Argument 'expr':
+ if (substitute) expr <- substitute(expr)
# Argument 'args':
if (!is.list(args)) {
diff --git a/R/withRepos.R b/R/withRepos.R
index ce304bb..5efa828 100644
--- a/R/withRepos.R
+++ b/R/withRepos.R
@@ -13,6 +13,8 @@
# \item{expr}{The R expression to be evaluated.}
# \item{repos}{A @character @vector of repositories to use.}
# \item{...}{Additional arguments passed to @see "useRepos".}
+# \item{substitute}{If @TRUE, argument \code{expr} is
+# \code{\link[base]{substitute}()}:ed, otherwise not.}
# \item{envir}{The @environment in which the expression should be evaluated.}
# }
#
@@ -50,9 +52,9 @@
# @keyword IO
# @keyword programming
#*/###########################################################################
-withRepos <- function(expr, repos="[[mainstream]]", ..., envir=parent.frame()) {
- # Argument '.expr':
- expr <- substitute(expr)
+withRepos <- function(expr, repos="[[mainstream]]", ..., substitute=TRUE, envir=parent.frame()) {
+ # Argument 'expr':
+ if (substitute) expr <- substitute(expr)
# Argument 'envir':
if (!is.environment(envir))
diff --git a/R/withSeed.R b/R/withSeed.R
index e5a1de6..9228809 100644
--- a/R/withSeed.R
+++ b/R/withSeed.R
@@ -12,6 +12,8 @@
# \arguments{
# \item{expr}{The R expression to be evaluated.}
# \item{seed, ...}{Arguments passed to @see "base::set.seed".}
+# \item{substitute}{If @TRUE, argument \code{expr} is
+# \code{\link[base]{substitute}()}:ed, otherwise not.}
# \item{envir}{The @environment in which the expression should be evaluated.}
# }
#
@@ -36,9 +38,9 @@
# @keyword IO
# @keyword programming
#*/###########################################################################
-withSeed <- function(expr, seed, ..., envir=parent.frame()) {
- # Argument '.expr':
- expr <- substitute(expr)
+withSeed <- function(expr, seed, ..., substitute=TRUE, envir=parent.frame()) {
+ # Argument 'expr':
+ if (substitute) expr <- substitute(expr)
# Argument 'envir':
if (!is.environment(envir))
diff --git a/R/withSink.R b/R/withSink.R
index c7c6a80..677c8d7 100644
--- a/R/withSink.R
+++ b/R/withSink.R
@@ -18,6 +18,8 @@
# \item{type}{A @character string specifying whether to divert output
# sent to the standard output or the standard error.
# See @see "base::sink" for details.}
+# \item{substitute}{If @TRUE, argument \code{expr} is
+# \code{\link[base]{substitute}()}:ed, otherwise not.}
# \item{envir}{The @environment in which the expression should be evaluated.}
# }
#
@@ -42,12 +44,12 @@
# @keyword IO
# @keyword programming
#*/###########################################################################
-withSink <- function(expr, file, append=FALSE, type=c("output", "message"), envir=parent.frame()) {
+withSink <- function(expr, file, append=FALSE, type=c("output", "message"), substitute=TRUE, envir=parent.frame()) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- # Argument '.expr':
- expr <- substitute(expr)
+ # Argument 'expr':
+ if (substitute) expr <- substitute(expr)
# Argument 'envir':
if (!is.environment(envir))
diff --git a/R/withTimeout.R b/R/withTimeout.R
index d1ce7c0..3ab42c9 100644
--- a/R/withTimeout.R
+++ b/R/withTimeout.R
@@ -12,6 +12,8 @@
#
# \arguments{
# \item{expr}{The R expression to be evaluated.}
+# \item{substitute}{If @TRUE, argument \code{expr} is
+# \code{\link[base]{substitute}()}:ed, otherwise not.}
# \item{envir}{The @environment in which the expression should
# be evaluated.}
# \item{timeout, cpu, elapsed}{A @numeric specifying the maximum number
@@ -44,10 +46,12 @@
# it is useful to know that it utilizes R's built-in time-out mechanism,
# which sets the limits on what is possible and not.
# From @see "base::setTimeLimit", we learn that:
+#
# \emph{"Time limits are checked whenever a user interrupt could occur.
-# This will happen frequently in R code and during Sys.sleep, but
+# This will happen frequently in R code and during Sys.sleep(*), but
# only at points in compiled C and Fortran code identified by the
# code author."}
+#
# More precisely, if a function is implemented in native code (e.g. C)
# and the developer of that function does not check for user interrupts,
# then you cannot interrupt that function neither via a user interrupt
@@ -59,6 +63,19 @@
# prompt (e.g. @see "base::readline" and @see "base::readLines") using
# timeouts; the timeout exception will not be thrown until after the user
# completes the prompt (i.e. after pressing ENTER).
+#
+# System calls via @see "base::system" and \code{system2()} cannot be
+# timed out via the above mechanisms. However, in \R (>= 3.5.0) these
+# functions have argument \code{timeout} providing their own independent
+# timeout mechanism.
+#
+# Other examples of calls that do \emph{not} support timeout are "atomic"
+# calls that may take very long such as large object allocation and
+# \code{rnorm(n)} where \code{n} is very large.
+#
+# (*) Note that on Unux and macOS, \code{Sys.sleep(time)} will signal a
+# timeout error only \emph{after} \code{time} seconds passed,
+# regardless of \code{timeout} limit (< \code{time}).
# }
#
# @author
@@ -66,8 +83,8 @@
# @examples "../incl/withTimeout.Rex"
#
# \seealso{
-# Internally, @see "base::eval" is used to evaluate the expression.
-# @see "base::setTimeLimit"
+# Internally, @see "base::eval" is used to evaluate the expression and
+# @see "base::setTimeLimit" is used to control for timeout events.
# }
#
# \references{
@@ -78,12 +95,12 @@
# @keyword IO
# @keyword programming
#*/###########################################################################
-withTimeout <- function(expr, envir=parent.frame(), timeout, cpu=timeout, elapsed=timeout, onTimeout=c("error", "warning", "silent"), ...) {
+withTimeout <- function(expr, substitute=TRUE, envir=parent.frame(), timeout, cpu=timeout, elapsed=timeout, onTimeout=c("error", "warning", "silent"), ...) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'expr':
- expr <- substitute(expr)
+ if (substitute) expr <- substitute(expr)
# Argument 'envir':
if (!is.environment(envir))
@@ -110,7 +127,8 @@ withTimeout <- function(expr, envir=parent.frame(), timeout, cpu=timeout, elapse
}, error = function(ex) {
msg <- ex$message;
# Was it a timeout?
- pattern <- gettext("reached elapsed time limit", domain="R")
+ pattern <- gettext("reached elapsed time limit", "reached CPU time limit", domain="R")
+ pattern <- paste(pattern, collapse = "|")
if (regexpr(pattern, msg) != -1L) {
ex <- TimeoutException(msg, cpu=cpu, elapsed=elapsed);
if (onTimeout == "error") {
@@ -127,7 +145,14 @@ withTimeout <- function(expr, envir=parent.frame(), timeout, cpu=timeout, elapse
} # withTimeout()
# BACKWARD COMPATIBILITY
-evalWithTimeout <- withTimeout
+evalWithTimeout <- local({
+ fcn <- withTimeout
+ expr <- body(fcn)
+ expr <- expr[c(1:2, 2:length(expr))]
+ expr[[2]] <- quote(.Deprecated(new = "withTimeout"))
+ body(fcn) <- expr
+ fcn
+})
############################################################################
diff --git a/man/as.character.binmode.Rd b/man/as.character.binmode.Rd
index fa587ca..d5768ba 100755
--- a/man/as.character.binmode.Rd
+++ b/man/as.character.binmode.Rd
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Do not modify this file since it was automatically generated from:
%
-% intToBin.R
+% intToHex.R
%
% by the Rdoc compiler part of the R.oo package.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/man/compressFile.Rd b/man/compressFile.Rd
index 087b7fb..dd1539d 100755
--- a/man/compressFile.Rd
+++ b/man/compressFile.Rd
@@ -81,7 +81,11 @@
Returns the pathname of the output file.
The number of bytes processed is returned as an attribute.
- \code{isCompressedFile()} etc. return a \code{\link[base]{logical}}.
+ \code{isCompressedFile()}, \code{isGzipped()} and \code{isBzipped()}
+ return a \code{\link[base]{logical}}.
+ Note that with \code{method = "extension"} (default), only the filename
+ extension is used to infer whether the file is compressed or not.
+ Specifically, it does not matter whether the file actually exists or not.
}
\details{
diff --git a/man/fileAccess.Rd b/man/fileAccess.Rd
index 75c3ea8..e106e60 100644
--- a/man/fileAccess.Rd
+++ b/man/fileAccess.Rd
@@ -116,7 +116,8 @@ print(fileAccess(pathname, mode=4))
\references{
[1] R-devel thread
\emph{file.access() on network (mounted) drive on Windows Vista?}
- on Nov 26, 2008.\cr
+ on Nov 26, 2008.
+ \url{https://stat.ethz.ch/pipermail/r-devel/2008-December/051461.html}\cr
[2] Filesystem permissions, Wikipedia, 2010.
\url{http://en.wikipedia.org/wiki/Filesystem_permissions}\cr
}
diff --git a/man/gcDLLs.Rd b/man/gcDLLs.Rd
index c823595..5e74cbf 100644
--- a/man/gcDLLs.Rd
+++ b/man/gcDLLs.Rd
@@ -23,10 +23,11 @@
}
\usage{
-gcDLLs(quiet=TRUE)
+gcDLLs(gc=TRUE, quiet=TRUE)
}
\arguments{
+ \item{gc}{If \code{\link[base:logical]{TRUE}}, if there are stray DLLs, then the garbage collector is run before unloading those DLLs. This is done in order to trigger any finalizers, of which some may need those DLLs, to be called.}
\item{quiet}{If \code{\link[base:logical]{FALSE}}, a message is outputted for every stray DLL that is unloaded.}
}
@@ -43,6 +44,11 @@ gcDLLs(quiet=TRUE)
following to your package:
\preformatted{
.onUnload <- function(libpath) {
+ ## (1) Force finalizers to be called before removing the DLL
+ ## in case some of them need the DLL.
+ gc()
+
+ ## (2) Unload the DLL for this package
library.dynam.unload(.packageName, libpath)
}
}
diff --git a/man/intToBin.Rd b/man/intToBin.Rd
index 4673cdb..32ed85f 100755
--- a/man/intToBin.Rd
+++ b/man/intToBin.Rd
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Do not modify this file since it was automatically generated from:
%
-% intToBin.R
+% intToHex.R
%
% by the Rdoc compiler part of the R.oo package.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -25,11 +25,27 @@
}
\arguments{
- \item{x}{An \code{\link[base]{integer}} to be converted.}
+ \item{x}{A \code{\link[base]{numeric}} vector of integers to be converted.}
}
\value{
- Returns a \code{\link[base]{character}}.
+Returns a \code{\link[base]{character}} string of length \code{length(x)}.
+For coercions out of range, \code{NA_character_} is returned for
+such elements.
+}
+
+\details{
+ For \code{length(x)} > 1, the number of characters in each of returned
+ elements is the same and driven by the \code{x} element that requires
+ the highest number of character - all other elements are padded with
+ zeros (or ones for negative values). This is why we for instance get
+ \code{intToHex(15) == "f"} but \code{intToHex(15:16) == c("0f", "10")}.
+
+ The supported range for \code{intToHex()}, \code{intToOct()}, and
+ \code{intToBin()} is that of \R integers, i.e.
+ \code{[-.Machine$integer.max, +.Machine$integer.max]} where.
+ \code{.Machine$integer.max} is \eqn{2^31-1}.
+ This limitation is there such that negative values can be converted too.
}
\author{Henrik Bengtsson}
diff --git a/man/isEof.connection.Rd b/man/isEof.connection.Rd
index 8562779..6d3cc38 100644
--- a/man/isEof.connection.Rd
+++ b/man/isEof.connection.Rd
@@ -29,6 +29,13 @@
Returns a \code{\link[base]{logical}}.
}
+\details{
+Internally \code{\link[base]{seek}}() is used, which according to to the \R help
+is discouraged on Windows. However, after many years of large-scale
+testing on various Windows versions and file systems we have yet to
+experience issues with using \code{seek()} on Windows.
+}
+
\author{Henrik Bengtsson}
\seealso{
diff --git a/man/isSingle.Rd b/man/isSingle.Rd
index 3f2c9dc..dce39c8 100644
--- a/man/isSingle.Rd
+++ b/man/isSingle.Rd
@@ -11,10 +11,10 @@
\alias{singles}
-\title{Identifies all entries that exists exactly ones}
+\title{Identifies all entries that exists exactly once}
\description{
- Identifies all entries that exists exactly ones.
+ Identifies all entries that exists exactly once.
}
\usage{
diff --git a/man/loadToEnv.Rd b/man/loadToEnv.Rd
index 5b573a3..adced43 100644
--- a/man/loadToEnv.Rd
+++ b/man/loadToEnv.Rd
@@ -17,7 +17,7 @@
}
\usage{
-\method{loadToEnv}{default}(..., envir=new.env())
+\method{loadToEnv}{default}(file, ..., envir=new.env())
}
\arguments{
diff --git a/man/nullfile.Rd b/man/nullfile.Rd
index a6997b3..4cc5827 100644
--- a/man/nullfile.Rd
+++ b/man/nullfile.Rd
@@ -13,7 +13,7 @@
\title{Gets the pathname of the NULL device on the current platform}
\description{
- Gets the pathname of the NULL device on the current platform. On Windows, it returns \code{"NIL"}. On all other
+ Gets the pathname of the NULL device on the current platform. On Windows, it returns \code{"NUL"}. On all other
platforms include Unix and macOS it returns \code{"/dev/null"}.
}
diff --git a/man/reassignInPackage.Rd b/man/reassignInPackage.Rd
index 86844fe..57f4e4c 100644
--- a/man/reassignInPackage.Rd
+++ b/man/reassignInPackage.Rd
@@ -24,8 +24,8 @@
\item{name}{The name of the object to be replaced."}
\item{pkgName}{The name of the package where the object lives."}
\item{value}{The new value to be assigned.}
- \item{keepOld}{If \code{\link[base:logical]{TRUE}}, the old value is kept as an attribute in
- the new object.}
+ \item{keepOld}{If \code{\link[base:logical]{TRUE}}, the old value is kept as attribute
+ \code{oldValue} in the new object.}
\item{...}{Not used.}
}
diff --git a/man/shell.exec2.Rd b/man/shell.exec2.Rd
index 47e6a13..52548e4 100644
--- a/man/shell.exec2.Rd
+++ b/man/shell.exec2.Rd
@@ -37,7 +37,7 @@ shell.exec2(file)
(i) unmaps any mapped drive letters used in the pathname
(e.g. 'X:/foo.bar.html' to 'C:/Users/Joe/bar.html'),
(ii) and replaces any forward slashed with backward ones
- (e.g. 'C:\\Users\\Joe\\bar.html' to 'C:/Users/Joe/bar.html').
+ (e.g. 'C:/Users/Joe/bar.html' to 'C:\\Users\\Joe\\bar.html').
URLs are passed as is to \code{shell.exec()}.
The reason for (i) is that some web browsers (e.g. Google Chrome)
diff --git a/man/use.Rd b/man/use.Rd
index cf38d9d..adefdfe 100644
--- a/man/use.Rd
+++ b/man/use.Rd
@@ -20,8 +20,9 @@
\usage{
\method{use}{default}(pkg="R.utils", version=NULL, how=c("attach", "load"), quietly=TRUE,
- warn.conflicts=!quietly, install=TRUE, repos=getOption("use/repos", c("[[current]]",
- "[[mainstream]]")), ..., verbose=FALSE)
+ warn.conflicts=!quietly, install=getOption("R.utils.use.install",
+ Sys.getenv("R_R_UTILS_USE_INSTALL", "TRUE")), repos=getOption("use/repos",
+ c("[[current]]", "[[mainstream]]")), ..., verbose=FALSE)
}
\arguments{
diff --git a/man/withCapture.Rd b/man/withCapture.Rd
index 6723fe7..0320597 100644
--- a/man/withCapture.Rd
+++ b/man/withCapture.Rd
@@ -18,14 +18,15 @@
}
\usage{
-withCapture(expr, substitute=getOption("withCapture/substitute", ".x."), code=TRUE,
+withCapture(expr, replace=getOption("withCapture/substitute", ".x."), code=TRUE,
output=code, ..., max.deparse.length=getOption("max.deparse.length", 10000), trim=TRUE,
- newline=getOption("withCapture/newline", TRUE), collapse="\n", envir=parent.frame())
+ newline=getOption("withCapture/newline", TRUE), collapse="\n", substitute=replace,
+ envir=parent.frame())
}
\arguments{
\item{expr}{The R expression to be evaluated.}
- \item{substitute}{An optional named \code{\link[base]{list}} used for substituting
+ \item{replace}{An optional named \code{\link[base]{list}} used for substituting
symbols with other strings.}
\item{code}{If \code{\link[base:logical]{TRUE}}, the deparsed code of the expression is echoed.}
\item{output}{If \code{\link[base:logical]{TRUE}}, the output of each evaluated subexpression
@@ -39,6 +40,7 @@ withCapture(expr, substitute=getOption("withCapture/substitute", ".x."), code=TR
is appended at the end.}
\item{collapse}{A \code{\link[base]{character}} string used for collapsing the captured
rows. If \code{\link[base]{NULL}}, the rows are not collapsed.}
+ \item{substitute}{(to be deprecated) use \code{replace} instead.}
\item{envir}{The \code{\link[base]{environment}} in which the expression is evaluated.}
}
@@ -78,7 +80,7 @@ print(withCapture({
# Automatic "variable" substitute
-# (disable with substitute=NULL)
+# (disable with relabel=NULL)
a <- 2
b <- "Hello world!"
diff --git a/man/withLocale.Rd b/man/withLocale.Rd
index b468b36..5a1c087 100644
--- a/man/withLocale.Rd
+++ b/man/withLocale.Rd
@@ -17,7 +17,7 @@
}
\usage{
-withLocale(expr, category, locale, ..., envir=parent.frame())
+withLocale(expr, category, locale, ..., substitute=TRUE, envir=parent.frame())
}
\arguments{
@@ -26,6 +26,8 @@ withLocale(expr, category, locale, ..., envir=parent.frame())
\item{locale}{\code{\link[base]{character}} \code{\link[base]{vector}} specifying the locale to used. The
first successfully set one will be used.}
\item{...}{Not used.}
+ \item{substitute}{If \code{\link[base:logical]{TRUE}}, argument \code{expr} is
+ \code{\link[base]{substitute}()}:ed, otherwise not.}
\item{envir}{The \code{\link[base]{environment}} in which the expression should be evaluated.}
}
diff --git a/man/withOptions.Rd b/man/withOptions.Rd
index e9f9d06..28c0033 100644
--- a/man/withOptions.Rd
+++ b/man/withOptions.Rd
@@ -17,13 +17,15 @@
}
\usage{
-withOptions(expr, ..., args=list(), envir=parent.frame())
+withOptions(expr, ..., args=list(), substitute=TRUE, envir=parent.frame())
}
\arguments{
\item{expr}{The R expression to be evaluated.}
\item{...}{Named options to be used.}
\item{args}{(optional) Additional named options specified as a named \code{\link[base]{list}}.}
+ \item{substitute}{If \code{\link[base:logical]{TRUE}}, argument \code{expr} is
+ \code{\link[base]{substitute}()}:ed, otherwise not.}
\item{envir}{The \code{\link[base]{environment}} in which the expression should be evaluated.}
}
diff --git a/man/withRepos.Rd b/man/withRepos.Rd
index 5560018..37bf268 100644
--- a/man/withRepos.Rd
+++ b/man/withRepos.Rd
@@ -17,13 +17,15 @@
}
\usage{
-withRepos(expr, repos="[[mainstream]]", ..., envir=parent.frame())
+withRepos(expr, repos="[[mainstream]]", ..., substitute=TRUE, envir=parent.frame())
}
\arguments{
\item{expr}{The R expression to be evaluated.}
\item{repos}{A \code{\link[base]{character}} \code{\link[base]{vector}} of repositories to use.}
\item{...}{Additional arguments passed to \code{\link{useRepos}}().}
+ \item{substitute}{If \code{\link[base:logical]{TRUE}}, argument \code{expr} is
+ \code{\link[base]{substitute}()}:ed, otherwise not.}
\item{envir}{The \code{\link[base]{environment}} in which the expression should be evaluated.}
}
diff --git a/man/withSeed.Rd b/man/withSeed.Rd
index 27960ab..e874325 100644
--- a/man/withSeed.Rd
+++ b/man/withSeed.Rd
@@ -17,12 +17,14 @@
}
\usage{
-withSeed(expr, seed, ..., envir=parent.frame())
+withSeed(expr, seed, ..., substitute=TRUE, envir=parent.frame())
}
\arguments{
\item{expr}{The R expression to be evaluated.}
\item{seed, ...}{Arguments passed to \code{\link[base]{set.seed}}().}
+ \item{substitute}{If \code{\link[base:logical]{TRUE}}, argument \code{expr} is
+ \code{\link[base]{substitute}()}:ed, otherwise not.}
\item{envir}{The \code{\link[base]{environment}} in which the expression should be evaluated.}
}
diff --git a/man/withSink.Rd b/man/withSink.Rd
index a0443df..6595568 100644
--- a/man/withSink.Rd
+++ b/man/withSink.Rd
@@ -17,7 +17,8 @@
}
\usage{
-withSink(expr, file, append=FALSE, type=c("output", "message"), envir=parent.frame())
+withSink(expr, file, append=FALSE, type=c("output", "message"), substitute=TRUE,
+ envir=parent.frame())
}
\arguments{
@@ -29,6 +30,8 @@ withSink(expr, file, append=FALSE, type=c("output", "message"), envir=parent.fra
\item{type}{A \code{\link[base]{character}} string specifying whether to divert output
sent to the standard output or the standard error.
See \code{\link[base]{sink}}() for details.}
+ \item{substitute}{If \code{\link[base:logical]{TRUE}}, argument \code{expr} is
+ \code{\link[base]{substitute}()}:ed, otherwise not.}
\item{envir}{The \code{\link[base]{environment}} in which the expression should be evaluated.}
}
diff --git a/man/withTimeout.Rd b/man/withTimeout.Rd
index 7fd45ed..186e4e2 100644
--- a/man/withTimeout.Rd
+++ b/man/withTimeout.Rd
@@ -18,12 +18,14 @@
}
\usage{
-withTimeout(expr, envir=parent.frame(), timeout, cpu=timeout, elapsed=timeout,
- onTimeout=c("error", "warning", "silent"), ...)
+withTimeout(expr, substitute=TRUE, envir=parent.frame(), timeout, cpu=timeout,
+ elapsed=timeout, onTimeout=c("error", "warning", "silent"), ...)
}
\arguments{
\item{expr}{The R expression to be evaluated.}
+ \item{substitute}{If \code{\link[base:logical]{TRUE}}, argument \code{expr} is
+ \code{\link[base]{substitute}()}:ed, otherwise not.}
\item{envir}{The \code{\link[base]{environment}} in which the expression should
be evaluated.}
\item{timeout, cpu, elapsed}{A \code{\link[base]{numeric}} specifying the maximum number
@@ -56,10 +58,12 @@ withTimeout(expr, envir=parent.frame(), timeout, cpu=timeout, elapsed=timeout,
it is useful to know that it utilizes R's built-in time-out mechanism,
which sets the limits on what is possible and not.
From \code{\link[base]{setTimeLimit}}(), we learn that:
+
\emph{"Time limits are checked whenever a user interrupt could occur.
- This will happen frequently in R code and during Sys.sleep, but
+ This will happen frequently in R code and during Sys.sleep(*), but
only at points in compiled C and Fortran code identified by the
code author."}
+
More precisely, if a function is implemented in native code (e.g. C)
and the developer of that function does not check for user interrupts,
then you cannot interrupt that function neither via a user interrupt
@@ -71,6 +75,19 @@ withTimeout(expr, envir=parent.frame(), timeout, cpu=timeout, elapsed=timeout,
prompt (e.g. \code{\link[base]{readline}}() and \code{\link[base]{readLines}}()) using
timeouts; the timeout exception will not be thrown until after the user
completes the prompt (i.e. after pressing ENTER).
+
+ System calls via \code{\link[base]{system}}() and \code{system2()} cannot be
+ timed out via the above mechanisms. However, in \R (>= 3.5.0) these
+ functions have argument \code{timeout} providing their own independent
+ timeout mechanism.
+
+ Other examples of calls that do \emph{not} support timeout are "atomic"
+ calls that may take very long such as large object allocation and
+ \code{rnorm(n)} where \code{n} is very large.
+
+ (*) Note that on Unux and macOS, \code{Sys.sleep(time)} will signal a
+ timeout error only \emph{after} \code{time} seconds passed,
+ regardless of \code{timeout} limit (< \code{time}).
}
\author{Henrik Bengtsson}
@@ -80,12 +97,12 @@ withTimeout(expr, envir=parent.frame(), timeout, cpu=timeout, elapsed=timeout,
# Function that takes "a long" time to run
# - - - - - - - - - - - - - - - - - - - - - - - - -
foo <- function() {
- print("Tic");
+ print("Tic")
for (kk in 1:100) {
- print(kk);
- Sys.sleep(0.1);
+ print(kk)
+ Sys.sleep(0.1)
}
- print("Tac");
+ print("Tac")
}
@@ -93,13 +110,13 @@ foo <- function() {
# Evaluate code, if it takes too long, generate
# a timeout by throwing a TimeoutException.
# - - - - - - - - - - - - - - - - - - - - - - - - -
-res <- NULL;
+res <- NULL
tryCatch({
res <- withTimeout({
- foo();
- }, timeout=1.08);
-}, TimeoutException=function(ex) {
- cat("Timeout. Skipping.\n");
+ foo()
+ }, timeout = 1.08)
+}, TimeoutException = function(ex) {
+ message("Timeout. Skipping.")
})
@@ -108,8 +125,14 @@ tryCatch({
# a timeout returning NULL and generate a warning.
# - - - - - - - - - - - - - - - - - - - - - - - - -
res <- withTimeout({
- foo();
-}, timeout=1.08, onTimeout="warning");
+ foo()
+}, timeout = 1.08, onTimeout = "warning")
+
+
+# The same using an expression object
+expr <- quote(foo())
+res <- withTimeout(expr, substitute = FALSE,
+ timeout = 1.08, onTimeout = "warning")
# - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -117,13 +140,13 @@ res <- withTimeout({
# a timeout, and return silently NULL.
# - - - - - - - - - - - - - - - - - - - - - - - - -
res <- withTimeout({
- foo();
-}, timeout=1.08, onTimeout="silent");
+ foo()
+}, timeout = 1.08, onTimeout = "silent")
}
\seealso{
- Internally, \code{\link[base]{eval}}() is used to evaluate the expression.
- \code{\link[base]{setTimeLimit}}()
+ Internally, \code{\link[base]{eval}}() is used to evaluate the expression and
+ \code{\link[base]{setTimeLimit}}() is used to control for timeout events.
}
\references{
diff --git a/tests/intToHex.R b/tests/intToHex.R
index fca862a..e53860d 100644
--- a/tests/intToHex.R
+++ b/tests/intToHex.R
@@ -1,11 +1,64 @@
library("R.utils")
-x <- 1:10
+x <- c(7, 8, 15, 16)
print(x)
+
y <- intToHex(x)
+y_truth <- c("07", "08", "0f", "10")
+print(y)
+stopifnot(is.character(y), all(!is.na(y)), identical(y, y_truth))
+
+y <- intToOct(x)
+y_truth <- c("07", "10", "17", "20")
print(y)
+stopifnot(is.character(y), all(!is.na(y)), identical(y, y_truth))
+
y <- intToBin(x)
+y_truth <- c("00111", "01000", "01111", "10000")
print(y)
+stopifnot(is.character(y), all(!is.na(y)), identical(y, y_truth))
+
+
+x <- -3:3
+print(x)
+
+y <- intToHex(x)
+y_truth <- c("fffffffd", "fffffffe", "ffffffff",
+ "00000000",
+ "00000001", "00000002", "00000003")
+print(y)
+stopifnot(is.character(y), all(!is.na(y)), identical(y, y_truth))
+
y <- intToOct(x)
+y_truth <- c("37777777775", "37777777776", "37777777777",
+ "00000000000",
+ "00000000001", "00000000002", "00000000003")
print(y)
+stopifnot(is.character(y), all(!is.na(y)), identical(y, y_truth))
+y <- intToBin(x)
+y_truth <- c("1111111111111111111111111111101",
+ "1111111111111111111111111111110",
+ "1111111111111111111111111111111",
+ "0000000000000000000000000000000",
+ "0000000000000000000000000000001",
+ "0000000000000000000000000000010",
+ "0000000000000000000000000000011")
+print(y)
+stopifnot(is.character(y), all(!is.na(y)), identical(y, y_truth))
+
+
+## Integer out of range
+x <- 2^31
+
+y <- intToBin(x)
+print(y)
+stopifnot(is.character(y), is.na(y))
+
+y <- intToHex(x)
+print(y)
+stopifnot(is.character(y), is.na(y))
+
+y <- intToOct(x)
+print(y)
+stopifnot(is.character(y), is.na(y))
diff --git a/tests/withCapture.R b/tests/withCapture.R
index 4a870e9..f77dd8f 100644
--- a/tests/withCapture.R
+++ b/tests/withCapture.R
@@ -43,6 +43,10 @@ stopifnot(bfr == "[1] 1\n")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Fixed substitutions
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+bfr <- withCapture({ x <- a }, replace=list(a="abc"))
+print(bfr)
+stopifnot(bfr == '> x <- "abc"\n')
+
bfr <- withCapture({ x <- a }, substitute=list(a="abc"))
print(bfr)
stopifnot(bfr == '> x <- "abc"\n')
diff --git a/tests/withTimeout.R b/tests/withTimeout.R
index e10c780..9820cbc 100644
--- a/tests/withTimeout.R
+++ b/tests/withTimeout.R
@@ -14,6 +14,10 @@ foo <- function() {
print("Tac")
}
+fib <- function(n) {
+ if (n == 0 | n == 1) return(n)
+ return (fib(n - 1) + fib(n - 2))
+}
# - - - - - - - - - - - - - - - - - - - - - - - - -
# Evaluate code, if it takes too long, generate
@@ -29,6 +33,19 @@ tryCatch({
})
# - - - - - - - - - - - - - - - - - - - - - - - - -
+# Evaluate code, if it takes too much CPU time,
+# generate a TimeoutException error.
+# - - - - - - - - - - - - - - - - - - - - - - - - -
+res <- NULL
+tryCatch({
+ res <- withTimeout({
+ fib(30)
+ }, cpu=0.1, elapsed=Inf)
+}, TimeoutException=function(ex) {
+ cat("Timeout (", ex$message, "). Skipping.\n", sep="")
+})
+
+# - - - - - - - - - - - - - - - - - - - - - - - - -
# Evaluate code, if it takes too long, generate
# a timeout warning.
# - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -41,6 +58,18 @@ tryCatch({
cat("Timeout warning (", ex$message, "). Skipping.\n", sep="")
})
+# - - - - - - - - - - - - - - - - - - - - - - - - -
+# Evaluate code, if it takes too much CPU time,
+# generate a timeout warning.
+# - - - - - - - - - - - - - - - - - - - - - - - - -
+res <- NULL
+tryCatch({
+ res <- withTimeout({
+ fib(30)
+ }, cpu=0.1, elapsed=Inf, onTimeout="warning")
+}, warning=function(ex) {
+ cat("Timeout warning (", ex$message, "). Skipping.\n", sep="")
+})
# - - - - - - - - - - - - - - - - - - - - - - - - -
# Evaluate code, if it takes too long, generate
@@ -76,6 +105,12 @@ tryCatch({
})
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Evalute expression
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+expr <- quote(cat("Hello world!\n"))
+res <- withTimeout(expr, substitute = FALSE, timeout=1.08)
+
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Visibility
--
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