BioC 3.2: CHECK report for gCMAP on moscato1

Package: gCMAP

Version: 1.14.0

Command: rm -rf gCMAP.buildbin-libdir gCMAP.Rcheck && mkdir gCMAP.buildbin-libdir gCMAP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.14.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.14.0.tar.gz

StartedAt: 2016-04-23 02:30:30 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:38:43 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 493.6 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf gCMAP.buildbin-libdir gCMAP.Rcheck && mkdir gCMAP.buildbin-libdir gCMAP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.14.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.14.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/gCMAP.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-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 '1.14.0'
* 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
'library' or 'require' calls in package code:
  'GO.db' 'KEGG.db' 'bigmemoryExtras'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
camera_score,eSet-CMAPCollection : .local: no visible global function
  definition for 'camera'
induceCMAPCollection,eSet : .local : <anonymous>: no visible global
  function definition for 'mwhich'
mroast_score,eSet-CMAPCollection : .local: no visible global function
  definition for 'mroast'
romer_score,eSet-CMAPCollection : .local: no visible global function
  definition for 'romer'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [60s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  28.22   0.21   29.19
romer_score-methods  9.14   0.00    9.15
** running examples for arch 'x64' ... [56s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  21.45   0.16   22.56
romer_score-methods 10.06   0.04   10.13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [38s]
 [38s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [37s]
 [38s] 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
* DONE

Status: 3 NOTEs
See
  'D:/biocbld/bbs-3.2-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_1.14.0.zip
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	0.36	0.01	0.37
CMAPResults-class	2.57	0.02	2.59
KEGG2cmap	0	0	0
SignedGeneSet-class	0.05	0.00	0.05
annotate_eset_list	0.15	0.00	0.15
camera_score-methods	0.69	0.02	0.71
center_eSet	0.06	0.01	0.08
connectivity_score-methods	0.28	0.00	0.28
eSetOnDisk	0.02	0.00	0.02
eset_instances	0.09	0.02	0.10
featureScores-methods	0.19	0.00	0.19
fisher_score-methods	0.21	0.00	0.22
gCMAPData-dataset	0.10	0.00	0.09
geneIndex-methods	0.08	0.01	0.10
generate_gCMAP_NChannelSet	0.23	0.02	0.25
gsealm_jg_score-methods	0.27	0.01	0.28
gsealm_score-methods	2.91	0.02	2.93
induceCMAPCollection-methods	0.05	0.01	0.06
mapNmerge	0	0	0
memorize	0	0	0
mergeCMAPs	0.10	0.00	0.11
mgsa_score-methods	28.22	0.21	29.19
minSetSize-methods	0.07	0.00	0.06
mroast_score-methods	0.79	0.00	0.79
romer_score-methods	9.14	0.00	9.15
signedRankSumTest	0	0	0
splitPerturbations	0.07	0.01	0.07
wilcox_score-methods	0.20	0.02	0.22

name	user	system	elapsed
CMAPCollection-class	0.39	0.00	0.39
CMAPResults-class	2.99	0.00	3.00
KEGG2cmap	0	0	0
SignedGeneSet-class	0.05	0.00	0.04
annotate_eset_list	0.13	0.00	0.13
camera_score-methods	0.49	0.02	0.51
center_eSet	0.04	0.00	0.04
connectivity_score-methods	0.21	0.00	0.21
eSetOnDisk	0	0	0
eset_instances	0.07	0.01	0.08
featureScores-methods	0.11	0.00	0.11
fisher_score-methods	0.16	0.00	0.15
gCMAPData-dataset	0.09	0.00	0.10
geneIndex-methods	0.09	0.00	0.09
generate_gCMAP_NChannelSet	0.29	0.00	0.28
gsealm_jg_score-methods	0.34	0.00	1.81
gsealm_score-methods	3.52	0.00	3.53
induceCMAPCollection-methods	0.07	0.00	0.06
mapNmerge	0	0	0
memorize	0	0	0
mergeCMAPs	0.17	0.00	0.17
mgsa_score-methods	21.45	0.16	22.56
minSetSize-methods	0.16	0.00	0.16
mroast_score-methods	1.50	0.02	1.51
romer_score-methods	10.06	0.04	10.13
signedRankSumTest	0.02	0.00	0.01
splitPerturbations	0.07	0.00	0.08
wilcox_score-methods	0.22	0.00	0.22