BioC 2.13: CHECK report for gCMAP on moscato1

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

* 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.

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)

name	user	system	elapsed
CMAPCollection-class	0.42	0.03	0.46
CMAPResults-class	3.73	0.03	3.79
KEGG2cmap	0.02	0.00	0.01
SignedGeneSet-class	0.09	0.00	0.10
annotate_eset_list	0.15	0.00	0.16
camera_score-methods	0.58	0.05	0.62
center_eSet	0.03	0.00	0.03
connectivity_score-methods	0.25	0.01	0.27
eSetOnDisk	0.01	0.00	0.01
eset_instances	0.08	0.00	0.08
featureScores-methods	0.19	0.00	0.19
fisher_score-methods	0.28	0.03	0.31
gCMAPData-dataset	0.09	0.02	0.11
geneIndex-methods	0.14	0.00	0.14
generate_gCMAP_NChannelSet	0.31	0.00	0.31
gsealm_jg_score-methods	0.31	0.01	0.32
gsealm_score-methods	3.11	0.00	3.11
induceCMAPCollection-methods	0.06	0.02	0.08
mapNmerge	0.02	0.00	0.02
memorize	0.02	0.00	0.01
mergeCMAPs	0.12	0.00	0.13
mgsa_score-methods	21.68	0.25	21.95
minSetSize-methods	0.11	0.00	0.11
mroast_score-methods	1.14	0.00	1.14
romer_score-methods	10.17	0.00	10.46
signedRankSumTest	0	0	0
splitPerturbations	0.10	0.00	0.09
wilcox_score-methods	0.26	0.00	0.27

name	user	system	elapsed
CMAPCollection-class	0.73	0.00	0.73
CMAPResults-class	5.37	0.03	5.40
KEGG2cmap	0.00	0.01	0.02
SignedGeneSet-class	0.15	0.00	0.15
annotate_eset_list	0.22	0.00	0.72
camera_score-methods	0.70	0.02	0.72
center_eSet	0.08	0.00	0.07
connectivity_score-methods	0.69	0.00	0.69
eSetOnDisk	0.03	0.00	0.03
eset_instances	0.11	0.02	0.12
featureScores-methods	0.23	0.00	0.24
fisher_score-methods	0.29	0.03	0.33
gCMAPData-dataset	0.18	0.01	0.20
geneIndex-methods	0.19	0.00	0.19
generate_gCMAP_NChannelSet	0.25	0.00	0.25
gsealm_jg_score-methods	0.52	0.00	0.88
gsealm_score-methods	4.96	0.02	4.97
induceCMAPCollection-methods	0.08	0.01	0.10
mapNmerge	0	0	0
memorize	0.01	0.00	0.01
mergeCMAPs	0.13	0.00	0.13
mgsa_score-methods	18.81	0.36	19.37
minSetSize-methods	0.11	0.00	0.11
mroast_score-methods	1.43	0.00	1.43
romer_score-methods	14.71	0.02	14.73
signedRankSumTest	0	0	0
splitPerturbations	0.17	0.00	0.17
wilcox_score-methods	0.30	0.00	0.29