BioC 3.1: CHECK report for gCMAP on zin2

Package: gCMAP

Version: 1.12.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.12.0.tar.gz

StartedAt: 2015-10-09 01:27:55 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:31:55 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 239.8 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/gCMAP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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
Package which this enhances but not available for checking: ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘gCMAP’ can be installed ... [19s/23s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/40s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  14.49  0.052   8.480
romer_score-methods  7.16  0.276   8.628
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [29s/35s]
 [29s/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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/gCMAP.Rcheck/00check.log’
for details.

* 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’
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	0.599	0.101	0.792
CMAPResults-class	1.977	0.048	2.278
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.040	0.000	0.039
annotate_eset_list	0.081	0.000	0.082
camera_score-methods	0.514	0.082	0.735
center_eSet	0.024	0.000	0.041
connectivity_score-methods	0.617	0.252	0.741
eSetOnDisk	0.004	0.000	0.008
eset_instances	0.059	0.000	0.095
featureScores-methods	0.117	0.029	0.349
fisher_score-methods	0.680	0.196	0.640
gCMAPData-dataset	0.273	0.075	0.371
geneIndex-methods	0.363	0.093	0.470
generate_gCMAP_NChannelSet	0.156	0.008	0.163
gsealm_jg_score-methods	0.664	0.180	0.568
gsealm_score-methods	2.266	0.099	2.993
induceCMAPCollection-methods	0.348	0.091	0.380
mapNmerge	0.001	0.000	0.000
memorize	0.004	0.000	0.004
mergeCMAPs	0.083	0.000	0.157
mgsa_score-methods	14.490	0.052	8.480
minSetSize-methods	0.887	0.280	1.176
mroast_score-methods	1.539	0.370	1.923
romer_score-methods	7.160	0.276	8.628
signedRankSumTest	0.002	0.000	0.002
splitPerturbations	0.060	0.003	0.132
wilcox_score-methods	0.646	0.309	0.907