[med-svn] r21702 - in trunk/packages/R/r-bioc-biocparallel/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Tue Apr 12 15:34:28 UTC 2016
Author: tille
Date: 2016-04-12 15:34:27 +0000 (Tue, 12 Apr 2016)
New Revision: 21702
Added:
trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/
trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/ignore_test_requiring_rmpi.patch
trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/series
Modified:
trunk/packages/R/r-bioc-biocparallel/trunk/debian/README.test
trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog
trunk/packages/R/r-bioc-biocparallel/trunk/debian/control
Log:
* New upstream version
* cme fix dpkg-control
* Add r-bioc-rsamtools to unit test dependency and Recommends of
the package
* Exclude requirement of Rmpi from tests since its not packaged yet
Closes: #820735
Modified: trunk/packages/R/r-bioc-biocparallel/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-biocparallel/trunk/debian/README.test 2016-04-12 12:11:33 UTC (rev 21701)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/README.test 2016-04-12 15:34:27 UTC (rev 21702)
@@ -10,5 +10,8 @@
in order to confirm its integrity. Make sure you have installed
the recommended package r-cran-doparallel before running the test.
+Please note: Rmpi is not packaged for Debian yet. So two tests
+requiring this package have been deleted from the test suite.
+
-- Andreas Tille <tille at debian.org> Mon, 30 Jun 2014 09:17:49 +0200
Modified: trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog 2016-04-12 12:11:33 UTC (rev 21701)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog 2016-04-12 15:34:27 UTC (rev 21702)
@@ -1,3 +1,14 @@
+r-bioc-biocparallel (1.4.3-1) unstable; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * Add r-bioc-rsamtools to unit test dependency and Recommends of
+ the package
+ * Exclude requirement of Rmpi from tests since its not packaged yet
+ Closes: #820735
+
+ -- Andreas Tille <tille at debian.org> Tue, 12 Apr 2016 15:32:10 +0200
+
r-bioc-biocparallel (1.4.0-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-biocparallel/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-biocparallel/trunk/debian/control 2016-04-12 12:11:33 UTC (rev 21701)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/control 2016-04-12 15:34:27 UTC (rev 21702)
@@ -12,8 +12,8 @@
r-cran-futile.logger,
r-cran-snow,
r-bioc-biocgenerics
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biocparallel/trunk/
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biocparallel/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biocparallel/trunk/
Homepage: http://bioconductor.org/packages/release/bioc/html/BiocParallel.html
@@ -26,7 +26,7 @@
r-cran-futile.logger,
r-cran-snow,
r-bioc-biocgenerics
-Recommends: r-cran-doparallel
+Recommends: r-cran-doparallel, r-bioc-rsamtools
Suggests: r-cran-mpi
Description: BioConductor facilities for parallel evaluation
This BioConductor package provides modified versions and novel
Added: trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/ignore_test_requiring_rmpi.patch
===================================================================
--- trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/ignore_test_requiring_rmpi.patch (rev 0)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/ignore_test_requiring_rmpi.patch 2016-04-12 15:34:27 UTC (rev 21702)
@@ -0,0 +1,63 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 Apr 2016 15:32:10 +0200
+Description: r-cran-mpi is not yet packages thus we can
+ not run the tests needing this package.
+ .
+ The according tests are removed in this patch.
+
+--- a/inst/unitTests/test_SnowParam.R
++++ b/inst/unitTests/test_SnowParam.R
+@@ -19,18 +19,6 @@ test_SnowParam_SOCK <- function()
+ checkIdentical(FALSE, bpisup(param))
+ }
+
+-test_SnowParam_MPI <- function()
+-{
+- if (.Platform$OS.type == "windows")
+- return()
+- param <- SnowParam(2, "MPI", tasks=2)
+- checkIdentical(FALSE, bpisup(param))
+-
+- exp <- bplapply(1:2, function(i) mpi.comm.rank(), BPPARAM=param)
+- checkIdentical(c(1L, 2L), sort(unlist(exp)))
+- checkIdentical(FALSE, bpisup(param))
+-}
+-
+ test_SnowParam_coerce_from_SOCK <- function()
+ {
+ if (!suppressWarnings(require(snow)))
+@@ -54,34 +42,6 @@ test_SnowParam_coerce_from_SOCK <- funct
+ checkIdentical(TRUE, bpisup(p))
+
+ parallel::stopCluster(cl)
+-}
+-
+-test_SnowParam_coerce_from_MPI <- function()
+-{
+- if (.Platform$OS.type == "windows")
+- return()
+- if (!(suppressWarnings(require(snow)) ||
+- suppressWarnings(require(Rmpi))))
+- ## quietly succeed if 'snow', 'Rmpi' not available
+- return()
+-
+- cl <- parallel::makeCluster(2L, "MPI")
+- p <- as(cl, "SnowParam")
+- checkTrue(validObject(p))
+-
+- obs <- tryCatch(bpstart(p), error=conditionMessage)
+- exp <- "'bpstart' not available; instance from outside BiocParallel?"
+- checkIdentical(exp, obs)
+-
+- obs <- tryCatch(bpstop(p), error=conditionMessage)
+- exp <- "'bpstop' not available; instance from outside BiocParallel?"
+- checkIdentical(exp, obs)
+-
+- exp <- bplapply(1:2, function(i) mpi.comm.rank(), BPPARAM=p)
+- checkIdentical(c(1L, 2L), sort(unlist(exp)))
+- checkIdentical(TRUE, bpisup(p))
+-
+- parallel::stopCluster(cl)
+ }
+
+ test_SnowParam_workers <- function()
Added: trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/series (rev 0)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/series 2016-04-12 15:34:27 UTC (rev 21702)
@@ -0,0 +1 @@
+ignore_test_requiring_rmpi.patch
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