BioC 3.5: CHECK report for gCMAP on tokay2

Package: gCMAP

Version: 1.19.0

Command: rm -rf gCMAP.buildbin-libdir gCMAP.Rcheck && mkdir gCMAP.buildbin-libdir gCMAP.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.19.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.19.0.tar.gz

StartedAt: 2017-01-01 22:41:53 -0500 (Sun, 01 Jan 2017)

EndedAt: 2017-01-01 22:47:17 -0500 (Sun, 01 Jan 2017)

EllapsedTime: 324.5 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.19.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out  && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.19.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/gCMAP.Rcheck'
* using R Under development (unstable) (2016-11-06 r71633)
* 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 '1.19.0'
* 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: no visible global function definition
  for 'camera'
induceCMAPCollection,eSet : <anonymous>: no visible global function
  definition for 'mwhich'
mroast_score,eSet-CMAPCollection: no visible global function definition
  for 'mroast'
romer_score,eSet-CMAPCollection: no visible global function definition
  for 'romer'
Undefined global functions or variables:
  camera mroast mwhich 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' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  14.58   0.25   16.45
romer_score-methods  5.05   0.05    5.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  15.76   0.28   16.12
romer_score-methods  5.53   0.02    5.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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
  'C:/Users/biocbuild/bbs-3.5-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_1.19.0.zip
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	0.24	0.01	0.25
CMAPResults-class	1.62	0.03	1.65
KEGG2cmap	0	0	0
SignedGeneSet-class	0.02	0.00	0.02
annotate_eset_list	0.08	0.00	0.08
camera_score-methods	0.25	0.02	0.26
center_eSet	0.01	0.00	0.02
connectivity_score-methods	0.11	0.00	0.11
eSetOnDisk	0.02	0.00	0.01
eset_instances	0.04	0.00	0.05
featureScores-methods	0.07	0.00	0.06
fisher_score-methods	0.09	0.00	0.10
gCMAPData-dataset	0.05	0.00	0.04
geneIndex-methods	0.03	0.00	0.04
generate_gCMAP_NChannelSet	0.09	0.02	0.11
gsealm_jg_score-methods	0.11	0.01	0.13
gsealm_score-methods	1.53	0.03	1.56
induceCMAPCollection-methods	0.03	0.00	0.03
mapNmerge	0	0	0
memorize	0.01	0.00	0.02
mergeCMAPs	0.10	0.00	0.09
mgsa_score-methods	14.58	0.25	16.45
minSetSize-methods	0.03	0.00	0.03
mroast_score-methods	0.45	0.05	0.50
romer_score-methods	5.05	0.05	5.10
signedRankSumTest	0	0	0
splitPerturbations	0.04	0.01	0.06
wilcox_score-methods	0.10	0.05	0.14

name	user	system	elapsed
CMAPCollection-class	0.59	0.03	0.63
CMAPResults-class	2.54	0.01	2.57
KEGG2cmap	0	0	0
SignedGeneSet-class	0.02	0.00	0.01
annotate_eset_list	0.11	0.02	0.13
camera_score-methods	0.36	0.01	0.37
center_eSet	0.01	0.00	0.02
connectivity_score-methods	0.14	0.00	0.14
eSetOnDisk	0.02	0.00	0.02
eset_instances	0.07	0.00	0.08
featureScores-methods	0.13	0.00	0.12
fisher_score-methods	0.19	0.02	0.21
gCMAPData-dataset	0.11	0.00	0.10
geneIndex-methods	0.11	0.00	0.11
generate_gCMAP_NChannelSet	0.24	0.02	0.25
gsealm_jg_score-methods	0.29	0.00	0.30
gsealm_score-methods	2.94	0.01	2.96
induceCMAPCollection-methods	0.04	0.00	0.04
mapNmerge	0	0	0
memorize	0	0	0
mergeCMAPs	0.11	0.00	0.11
mgsa_score-methods	15.76	0.28	16.12
minSetSize-methods	0.05	0.02	0.06
mroast_score-methods	0.89	0.01	0.91
romer_score-methods	5.53	0.02	5.55
signedRankSumTest	0	0	0
splitPerturbations	0.06	0.00	0.07
wilcox_score-methods	0.16	0.01	0.17