[med-svn] [r-cran-globals] 01/06: New upstream version 0.7.1
Andreas Tille
tille at debian.org
Tue Nov 8 08:55:16 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-globals.
commit 9691387c8a33ed9d7cf58ce821752b0b8930422c
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 8 09:46:43 2016 +0100
New upstream version 0.7.1
---
DESCRIPTION | 2 +-
NEWS | 8 ++++++
R/Globals-class.R | 17 ++++++++-----
R/walkAST.R | 6 ++++-
cran-comments.md | 17 +++++++------
revdep/README.md | 71 +++++++++++++++++++++++++++++++++--------------------
revdep/checks.rds | Bin 8337 -> 8451 bytes
revdep/problems.md | 7 ++++--
revdep/timing.md | 26 ++++++++++++++++++++
tests/Globals.R | 9 +++++++
tests/walkAST.R | 1 +
11 files changed, 119 insertions(+), 45 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 9bc40f3..5b51f0a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: globals
-Version: 0.7.0
+Version: 0.7.1
Depends:
R (>= 3.1.2)
Imports:
diff --git a/NEWS b/NEWS
index 97be795..1a900e2 100644
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,14 @@
Package: globals
================
+Version: 0.7.1 [2016-10-13]
+o Globals() and as.Globals() now accepts an empty list
+ as input as well.
+o BUG FIX: walkAST(quote( function(x=NULL) 0 )) would give
+ a sanity check error due to the NULL argument. Thank
+ you GitHub user billy34 for reporting on this.
+
+
Version: 0.7.0 [2016-09-08]
o Added walkAST(), which can be used to tweak expressions.
o Added globalsByName() for locating and retrieving a set of
diff --git a/R/Globals-class.R b/R/Globals-class.R
index 9bc8695..7732a03 100644
--- a/R/Globals-class.R
+++ b/R/Globals-class.R
@@ -13,19 +13,24 @@
#'
#' @aliases as.Globals as.Globals.Globals as.Globals.list [.Globals names
#' @export
-Globals <- function(object, ...) {
+Globals <- function(object=list(), ...) {
if (!is.list(object)) {
stop("Argument 'object' is not a list: ", class(object)[1])
}
- names <- names(object)
- if (is.null(names)) {
- stop("Argument 'object' must be a named list.")
- } else if (!all(nzchar(names))) {
- stop("Argument 'object' specifies globals with empty names.")
+ if (length(object) > 0) {
+ names <- names(object)
+ if (is.null(names)) {
+ stop("Argument 'object' must be a named list.")
+ } else if (!all(nzchar(names))) {
+ stop("Argument 'object' specifies globals with empty names.")
+ }
}
where <- attr(object, "where")
+ if (length(object) == 0 && is.null(where)) {
+ attr(object, "where") <- where <- list()
+ }
stopifnot(is.list(where))
## TODO: Add only when future (> 1.0.1) is on CRAN /HB 2016-09-05
diff --git a/R/walkAST.R b/R/walkAST.R
index 8e67dcf..56a8372 100644
--- a/R/walkAST.R
+++ b/R/walkAST.R
@@ -43,7 +43,11 @@ walkAST <- function(expr, atomic=NULL, name=NULL, call=NULL, pairlist=NULL, subs
expr[[pp]] <- e
}
}
- if (is.function(pairlist)) expr <- pairlist(expr)
+ ## WORKAROUND: Since expr[i] <- list(NULL) turns pairlist 'expr' into
+ ## a list we have to make sure to it is a pairlist also afterward, cf.
+ ## https://stat.ethz.ch/pipermail/r-devel/2016-October/073263.html
+ ## /HB 2016-10-12
+ expr <- as.pairlist(expr)
} else {
stop("Cannot walk expression. Unknown object type ", sQuote(typeof(expr)), call.=FALSE)
}
diff --git a/cran-comments.md b/cran-comments.md
index b006a3e..7eed485 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +1,5 @@
-# CRAN submission globals 0.7.0
-on 2016-09-08
+# CRAN submission globals 0.7.1
+on 2016-10-13
I've verified that this submission causes *no* issues for
any of the 20 reverse (recursive) package dependencies
@@ -21,26 +21,27 @@ The package has been verified using `R CMD check --as-cran` on:
* Platform x86_64-unknown-linux-gnu (64-bit) [Travis CI]:
- R version 3.2.5 (2016-04-14)
- R version 3.3.1 (2016-06-21)
- - R Under development (unstable) (2016-09-07 r71224)
+ - R Under development (unstable) (2016-10-12 r71502)
* Platform x86_64-pc-linux-gnu (64-bit):
+ - R version 3.1.2 (2014-10-31)
- R version 3.2.5 (2016-04-14)
- R version 3.3.1 (2016-06-21)
- - R version 3.3.1 Patched (2016-09-07 r71224)
- - R Under development (unstable) (2016-09-07 r71224)
+ - R version 3.3.1 Patched (2016-10-12 r71510)
+ - R Under development (unstable) (2016-10-12 r71510)
* Platform i686-pc-linux-gnu (32-bit):
- R version 3.3.1 (2016-06-21)
* Platform i386-w64-mingw32 (32-bit) [Appveyor CI]:
- - R Under development (unstable) (2016-09-06 r71220)
+ - R Under development (unstable) (2016-10-10 r71494)
* Platform x86_64-w64-mingw32/x64 (64-bit) [Appveyor CI]:
- - R Under development (unstable) (2016-09-06 r71220)
+ - R Under development (unstable) (2016-10-10 r71494)
* Platform x86_64-w64-mingw32/x64 (64-bit) [win-builder]:
- R version 3.3.1 (2016-06-21)
- - R Under development (unstable) (2016-09-08 r71224)
+ - R Under development (unstable) (2016-10-13 r71511)
### Reverse package check validation
diff --git a/revdep/README.md b/revdep/README.md
index 09f246d..e4206fd 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -10,17 +10,41 @@
|language |en |
|collate |en_US.UTF-8 |
|tz |SystemV/PST8PDT |
-|date |2016-09-08 |
+|date |2016-10-13 |
## Packages
|package |* |version |date |source |
|:-------|:--|:----------|:----------|:----------------------------------|
-|globals | |0.6.1-9000 |2016-09-08 |local (HenrikBengtsson/globals at NA) |
+|globals | |0.7.0-9000 |2016-10-14 |local (HenrikBengtsson/globals at NA) |
# Check results
+
20 packages
+|package |version | errors| warnings| notes|
+|:----------------|:-------|------:|--------:|-----:|
+|ACNE |0.8.1 | 0| 0| 0|
+|aroma.affymetrix |3.0.0 | 0| 0| 0|
+|aroma.cn |1.6.1 | 0| 0| 0|
+|aroma.core |3.0.0 | 0| 0| 1|
+|calmate |0.12.1 | 0| 0| 0|
+|doFuture |0.2.1 | 0| 0| 0|
+|fiery |0.2.1 | 0| 0| 0|
+|future.BatchJobs |0.13.0 | 0| 0| 0|
+|future |1.1.1 | 0| 0| 0|
+|GeneBreak |1.3.0 | 0| 0| 1|
+|MPAgenomics |1.1.2 | 0| 0| 2|
+|NSA |0.0.32 | 0| 0| 6|
+|pbmcapply |1.1.1 | 0| 0| 0|
+|PECA |1.9.0 | 0| 0| 1|
+|PSCBS |0.61.0 | 0| 0| 0|
+|PureCN |1.1.56 | 0| 0| 1|
+|QDNAseq |1.9.2 | 0| 0| 0|
+|Repitools |1.19.3 | 0| 0| 2|
+|R.filesets |2.10.0 | 0| 0| 0|
+|TIN |1.5.2 | 0| 0| 2|
+
## ACNE (0.8.1)
Maintainer: Henrik Bengtsson <henrikb at braju.com>
Bug reports: https://github.com/HenrikBengtsson/ACNE/issues
@@ -75,13 +99,13 @@ Bug reports: https://github.com/HenrikBengtsson/future.BatchJobs/issues
0 errors | 0 warnings | 0 notes
-## future (1.0.1)
+## future (1.1.1)
Maintainer: Henrik Bengtsson <henrikb at braju.com>
Bug reports: https://github.com/HenrikBengtsson/future/issues
0 errors | 0 warnings | 0 notes
-## GeneBreak (1.2.0)
+## GeneBreak (1.3.0)
Maintainer: Evert van den Broek <vandenbroek.evert at gmail.com>
0 errors | 0 warnings | 1 note
@@ -221,13 +245,13 @@ Rd file 'NSANormalization.Rd':
These lines will be truncated in the PDF manual.
```
-## pbmcapply (1.1.0)
+## pbmcapply (1.1.1)
Maintainer: Kevin kuang <kvn.kuang at mail.utoronto.ca>
Bug reports: https://github.com/kvnkuang/pbmcapply/issues
0 errors | 0 warnings | 0 notes
-## PECA (1.8.0)
+## PECA (1.9.0)
Maintainer: Tomi Suomi <tomi.suomi at utu.fi>
0 errors | 0 warnings | 1 note
@@ -247,7 +271,7 @@ Bug reports: https://github.com/HenrikBengtsson/PSCBS/issues
0 errors | 0 warnings | 0 notes
-## PureCN (1.0.4)
+## PureCN (1.1.56)
Maintainer: Markus Riester <markus.riester at novartis.com>
0 errors | 0 warnings | 1 note
@@ -255,9 +279,17 @@ Maintainer: Markus Riester <markus.riester at novartis.com>
```
checking R code for possible problems ... NOTE
Found the following calls to data() loading into the global environment:
+File ‘PureCN/R/bootstrapResults.R’:
+ data(purecn.example.output)
+File ‘PureCN/R/callAlterations.R’:
+ data(purecn.example.output)
+ data(purecn.example.output)
+File ‘PureCN/R/callLOH.R’:
+ data(purecn.example.output)
File ‘PureCN/R/createCurationFile.R’:
data(purecn.example.output)
-File ‘PureCN/R/findFocal.R’:
+File ‘PureCN/R/curateResults.R’:
+ data(purecn.example.output)
data(purecn.example.output)
File ‘PureCN/R/plotAbs.R’:
data(purecn.example.output)
@@ -265,31 +297,16 @@ File ‘PureCN/R/predictSomatic.R’:
data(purecn.example.output)
File ‘PureCN/R/readCurationFile.R’:
data(purecn.example.output)
-File ‘PureCN/R/runAbsoluteCN.R’:
- data(purecn.example.output)
-File ‘PureCN/R/segmentationCBS.R’:
- data(purecn.example.output)
See section ‘Good practice’ in ‘?data’.
```
-## QDNAseq (1.8.0)
+## QDNAseq (1.9.2)
Maintainer: Daoud Sie <d.sie at vumc.nl>
Bug reports: https://github.com/ccagc/QDNAseq/issues
-0 errors | 0 warnings | 1 note
-
-```
-checking R code for possible problems ... NOTE
-estimateCorrection,QDNAseqReadCounts : calculateFits: no visible global
- function definition for ‘formula’
-Undefined global functions or variables:
- formula
-Consider adding
- importFrom("stats", "formula")
-to your NAMESPACE file.
-```
+0 errors | 0 warnings | 0 notes
-## Repitools (1.18.2)
+## Repitools (1.19.3)
Maintainer: Mark Robinson <mark.robinson at imls.uzh.ch>
0 errors | 0 warnings | 2 notes
@@ -348,7 +365,7 @@ Bug reports: https://github.com/HenrikBengtsson/R.filesets/issues
0 errors | 0 warnings | 0 notes
-## TIN (1.4.1)
+## TIN (1.5.2)
Maintainer: Bjarne Johannessen <bjajoh at rr-research.no>
0 errors | 0 warnings | 2 notes
diff --git a/revdep/checks.rds b/revdep/checks.rds
index df04acf..bb8f5a4 100644
Binary files a/revdep/checks.rds and b/revdep/checks.rds differ
diff --git a/revdep/problems.md b/revdep/problems.md
index 2dd5396..9de1c06 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -10,15 +10,18 @@
|language |en |
|collate |en_US.UTF-8 |
|tz |SystemV/PST8PDT |
-|date |2016-09-08 |
+|date |2016-10-13 |
## Packages
|package |* |version |date |source |
|:-------|:--|:----------|:----------|:----------------------------------|
-|globals | |0.6.1-9000 |2016-09-08 |local (HenrikBengtsson/globals at NA) |
+|globals | |0.7.0-9000 |2016-10-14 |local (HenrikBengtsson/globals at NA) |
# Check results
+
0 packages with problems
+
+
diff --git a/revdep/timing.md b/revdep/timing.md
new file mode 100644
index 0000000..e749f88
--- /dev/null
+++ b/revdep/timing.md
@@ -0,0 +1,26 @@
+# Check times
+
+| |package |version | check_time|
+|:--|:----------------|:-------|----------:|
+|16 |PureCN |1.1.56 | 846.1|
+|18 |Repitools |1.19.3 | 484.7|
+|15 |PSCBS |0.61.0 | 335.2|
+|9 |future |1.1.1 | 332.5|
+|17 |QDNAseq |1.9.2 | 274.2|
+|7 |fiery |0.2.1 | 257.6|
+|20 |TIN |1.5.2 | 246.9|
+|2 |aroma.affymetrix |3.0.0 | 205.9|
+|14 |PECA |1.9.0 | 189.9|
+|10 |GeneBreak |1.3.0 | 169.2|
+|19 |R.filesets |2.10.0 | 167.5|
+|4 |aroma.core |3.0.0 | 140.2|
+|6 |doFuture |0.2.1 | 137.6|
+|8 |future.BatchJobs |0.13.0 | 123|
+|3 |aroma.cn |1.6.1 | 68.3|
+|11 |MPAgenomics |1.1.2 | 65.5|
+|5 |calmate |0.12.1 | 57.4|
+|1 |ACNE |0.8.1 | 53.8|
+|12 |NSA |0.0.32 | 37.6|
+|13 |pbmcapply |1.1.1 | 15.5|
+
+
diff --git a/tests/Globals.R b/tests/Globals.R
index d6af4e0..fd61b1a 100644
--- a/tests/Globals.R
+++ b/tests/Globals.R
@@ -225,6 +225,15 @@ stopifnot(
message("*** Globals() - coercion ... DONE")
+message("*** Globals() - empty ...")
+
+globals <- Globals()
+globals <- Globals(list())
+globals <- as.Globals(list())
+
+message("*** Globals() - empty ... DONE")
+
+
message("*** Globals() - exceptions ...")
res <- tryCatch({ Globals(NULL) }, error = identity)
diff --git a/tests/walkAST.R b/tests/walkAST.R
index 86f1f9e..245c820 100644
--- a/tests/walkAST.R
+++ b/tests/walkAST.R
@@ -18,6 +18,7 @@ exprs <- list(
fcn = substitute(function(a=1, b=2) sum(c(a, b))),
fcn = substitute(function(a=1, b) sum(c(a, b))),
fcn = substitute(function(a=1, b=2, ...) sum(c(a, b, ...))),
+ fcn = substitute(function(a=NULL) a),
ok = substitute(function(...) sum(x, ...)),
warn = substitute(sum(x, ...)),
null = substitute(NULL)
--
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