[med-svn] r21870 - in trunk/packages/R/r-bioc-biocparallel/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-05-08 06:56:05 +0000 (Sun, 08 May 2016)
New Revision: 21870

Modified:
   trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog
   trunk/packages/R/r-bioc-biocparallel/trunk/debian/control
   trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/ignore_test_requiring_rmpi.patch
Log:
New upstream version


Modified: trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog	2016-05-08 06:52:49 UTC (rev 21869)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/changelog	2016-05-08 06:56:05 UTC (rev 21870)
@@ -1,3 +1,10 @@
+r-bioc-biocparallel (1.6.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org>  Sun, 08 May 2016 08:41:08 +0200
+
 r-bioc-biocparallel (1.4.3-1) 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	2016-05-08 06:52:49 UTC (rev 21869)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/control	2016-05-08 06:56:05 UTC (rev 21870)
@@ -12,7 +12,7 @@
                r-cran-futile.logger,
                r-cran-snow,
                r-bioc-biocgenerics
-Standards-Version: 3.9.7
+Standards-Version: 3.9.8
 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 +26,8 @@
          r-cran-futile.logger,
          r-cran-snow,
          r-bioc-biocgenerics
-Recommends: r-cran-doparallel, r-bioc-rsamtools
+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

Modified: 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	2016-05-08 06:52:49 UTC (rev 21869)
+++ trunk/packages/R/r-bioc-biocparallel/trunk/debian/patches/ignore_test_requiring_rmpi.patch	2016-05-08 06:56:05 UTC (rev 21870)
@@ -7,14 +7,17 @@
 
 --- a/inst/unitTests/test_SnowParam.R
 +++ b/inst/unitTests/test_SnowParam.R
-@@ -19,18 +19,6 @@ test_SnowParam_SOCK <- function()
-     checkIdentical(FALSE, bpisup(param))
+@@ -24,21 +24,6 @@ test_SnowParam_SOCK_character <- functio
+     bpstop(bpstart(SnowParam("localhost")))
  }
  
 -test_SnowParam_MPI <- function() 
 -{
 -    if (.Platform$OS.type == "windows")
--        return()
+-        DEACTIVATED("MPI tests not run on Windows")
+-
+-    DEACTIVATED("MPI tests not run")
+-
 -    param <- SnowParam(2, "MPI", tasks=2)
 -    checkIdentical(FALSE, bpisup(param))
 -
@@ -25,8 +28,8 @@
 -
  test_SnowParam_coerce_from_SOCK <- function()
  {
-     if (!suppressWarnings(require(snow)))
-@@ -54,34 +42,6 @@ test_SnowParam_coerce_from_SOCK <- funct
+     if (!requireNamespace("snow", quietly=TRUE))
+@@ -61,36 +46,6 @@ test_SnowParam_coerce_from_SOCK <- funct
      checkIdentical(TRUE, bpisup(p))
  
      parallel::stopCluster(cl)
@@ -35,12 +38,14 @@
 -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()
+-        DEACTIVATED("MPI tests not run on Windows")
+-    
+-    if (!requireNamespace("snow", quietly=TRUE) ||
+-         !requireNamespace("Rmpi", quietly=TRUE))
+-        DEACTIVATED("'snow' and/or 'Rmpi' package did not load")
 -
+-    DEACTIVATED("MPI tests not run")
+-
 -    cl <- parallel::makeCluster(2L, "MPI")
 -    p <- as(cl, "SnowParam")
 -    checkTrue(validObject(p))