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BioC 2.13: CHECK report for gCMAP on moscato1

This page was generated on 2014-04-05 09:51:01 -0700 (Sat, 05 Apr 2014).

Package 275/750HostnameOS / ArchBUILDCHECKBUILD BIN
gCMAP 1.6.0
Thomas Sandmann
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/gCMAP
Last Changed Rev: 83286 / Revision: 88450
Last Changed Date: 2013-11-13 21:35:59 -0800 (Wed, 13 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: gCMAP
Version: 1.6.0
Command: rm -rf gCMAP.buildbin-libdir && mkdir gCMAP.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.6.0.tar.gz >gCMAP-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.6.0.tar.gz && mv gCMAP.buildbin-libdir/* gCMAP.Rcheck/ && rmdir gCMAP.buildbin-libdir
StartedAt: 2014-04-05 04:00:45 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:09:13 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 508.1 seconds
RetCode: 0
Status:  OK  
CheckDir: gCMAP.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/gCMAP.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gCMAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gCMAP' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'bigmemory' 'bigmemoryExtras'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'gCMAP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'Biobase' 'BiocGenerics' 'Category' 'annotate' 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'GSEABase' 'limma'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'GSEABase:::.showGeneSet'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'CMAPResults'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eSetOnDisk: no visible global function definition for 'BigMatrix'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'diffExprAnalysis.Rnw', 'gCMAP.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [54s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  21.68   0.25   21.95
romer_score-methods 10.17   0.00   10.46
** running examples for arch 'x64' ... [65s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  18.81   0.36   19.37
romer_score-methods 14.71   0.02   14.73
CMAPResults-class    5.37   0.03    5.40
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [39s]
 [39s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [43s]
 [44s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/gCMAP.Rcheck/00check.log'
for details.

gCMAP.Rcheck/00install.out:


install for i386

* installing *source* package 'gCMAP' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'gCMAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gCMAP' as gCMAP_1.6.0.zip
* DONE (gCMAP)

gCMAP.Rcheck/examples_i386/gCMAP-Ex.timings:

nameusersystemelapsed
CMAPCollection-class0.420.030.46
CMAPResults-class3.730.033.79
KEGG2cmap0.020.000.01
SignedGeneSet-class0.090.000.10
annotate_eset_list0.150.000.16
camera_score-methods0.580.050.62
center_eSet0.030.000.03
connectivity_score-methods0.250.010.27
eSetOnDisk0.010.000.01
eset_instances0.080.000.08
featureScores-methods0.190.000.19
fisher_score-methods0.280.030.31
gCMAPData-dataset0.090.020.11
geneIndex-methods0.140.000.14
generate_gCMAP_NChannelSet0.310.000.31
gsealm_jg_score-methods0.310.010.32
gsealm_score-methods3.110.003.11
induceCMAPCollection-methods0.060.020.08
mapNmerge0.020.000.02
memorize0.020.000.01
mergeCMAPs0.120.000.13
mgsa_score-methods21.68 0.2521.95
minSetSize-methods0.110.000.11
mroast_score-methods1.140.001.14
romer_score-methods10.17 0.0010.46
signedRankSumTest000
splitPerturbations0.100.000.09
wilcox_score-methods0.260.000.27

gCMAP.Rcheck/examples_x64/gCMAP-Ex.timings:

nameusersystemelapsed
CMAPCollection-class0.730.000.73
CMAPResults-class5.370.035.40
KEGG2cmap0.000.010.02
SignedGeneSet-class0.150.000.15
annotate_eset_list0.220.000.72
camera_score-methods0.700.020.72
center_eSet0.080.000.07
connectivity_score-methods0.690.000.69
eSetOnDisk0.030.000.03
eset_instances0.110.020.12
featureScores-methods0.230.000.24
fisher_score-methods0.290.030.33
gCMAPData-dataset0.180.010.20
geneIndex-methods0.190.000.19
generate_gCMAP_NChannelSet0.250.000.25
gsealm_jg_score-methods0.520.000.88
gsealm_score-methods4.960.024.97
induceCMAPCollection-methods0.080.010.10
mapNmerge000
memorize0.010.000.01
mergeCMAPs0.130.000.13
mgsa_score-methods18.81 0.3619.37
minSetSize-methods0.110.000.11
mroast_score-methods1.430.001.43
romer_score-methods14.71 0.0214.73
signedRankSumTest000
splitPerturbations0.170.000.17
wilcox_score-methods0.300.000.29