BioC 3.1: CHECK report for gCMAP on moscato2

Package: gCMAP

Version: 1.12.0

Command: rm -rf gCMAP.buildbin-libdir gCMAP.Rcheck && mkdir gCMAP.buildbin-libdir gCMAP.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.12.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.12.0.tar.gz

StartedAt: 2015-10-09 01:55:36 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:02:35 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 419.0 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.12.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.12.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/gCMAP.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.12.0'
* 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' ... [55s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  27.16   0.24   27.55
romer_score-methods  8.98   0.01    9.00
** running examples for arch 'x64' ... [51s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  22.64   0.17   22.93
romer_score-methods  8.86   0.03    8.90
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [36s]
 [36s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [35s]
 [35s] 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
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'gCMAP' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'gCMAP' as gCMAP_1.12.0.zip
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	0.33	0.00	0.33
CMAPResults-class	2.67	0.00	2.67
KEGG2cmap	0	0	0
SignedGeneSet-class	0.08	0.00	0.08
annotate_eset_list	0.17	0.00	0.17
camera_score-methods	0.61	0.01	0.62
center_eSet	0.03	0.02	0.05
connectivity_score-methods	0.27	0.00	0.27
eSetOnDisk	0	0	0
eset_instances	0.11	0.00	0.11
featureScores-methods	0.16	0.00	0.16
fisher_score-methods	0.2	0.0	0.2
gCMAPData-dataset	0.11	0.00	0.11
geneIndex-methods	0.09	0.00	0.09
generate_gCMAP_NChannelSet	0.27	0.00	0.27
gsealm_jg_score-methods	0.33	0.02	0.34
gsealm_score-methods	2.99	0.01	3.01
induceCMAPCollection-methods	0.05	0.00	0.05
mapNmerge	0	0	0
memorize	0	0	0
mergeCMAPs	0.09	0.00	0.09
mgsa_score-methods	27.16	0.24	27.55
minSetSize-methods	0.05	0.01	0.06
mroast_score-methods	0.92	0.02	0.94
romer_score-methods	8.98	0.01	9.00
signedRankSumTest	0	0	0
splitPerturbations	0.13	0.00	0.13
wilcox_score-methods	0.22	0.00	0.21

name	user	system	elapsed
CMAPCollection-class	0.50	0.01	0.52
CMAPResults-class	3.48	0.02	3.50
KEGG2cmap	0	0	0
SignedGeneSet-class	0.08	0.00	0.08
annotate_eset_list	0.15	0.02	0.17
camera_score-methods	0.66	0.03	0.69
center_eSet	0.05	0.00	0.04
connectivity_score-methods	0.29	0.00	0.30
eSetOnDisk	0	0	0
eset_instances	0.11	0.00	0.11
featureScores-methods	0.14	0.01	0.16
fisher_score-methods	0.22	0.00	0.22
gCMAPData-dataset	0.09	0.02	0.11
geneIndex-methods	0.11	0.00	0.11
generate_gCMAP_NChannelSet	0.26	0.00	0.26
gsealm_jg_score-methods	0.36	0.00	0.36
gsealm_score-methods	3.2	0.0	3.2
induceCMAPCollection-methods	0.08	0.00	0.08
mapNmerge	0	0	0
memorize	0.01	0.00	0.01
mergeCMAPs	0.14	0.00	0.14
mgsa_score-methods	22.64	0.17	22.93
minSetSize-methods	0.12	0.00	0.12
mroast_score-methods	0.87	0.02	0.89
romer_score-methods	8.86	0.03	8.90
signedRankSumTest	0.02	0.00	0.01
splitPerturbations	0.08	0.00	0.08
wilcox_score-methods	0.28	0.00	0.28