BioC 3.2: CHECK report for gCMAP on oaxaca

Package: gCMAP

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.14.0.tar.gz

StartedAt: 2015-10-27 03:49:41 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:54:14 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 272.5 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gCMAP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.14.0’
* 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 ... [26s/27s] 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 ... [52s/55s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  12.599  0.310  22.556
romer_score-methods  5.805  0.681   6.354
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [40s/35s]
 [41s/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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/gCMAP.Rcheck/00check.log’
for details.

* 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
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	1.129	0.377	1.121
CMAPResults-class	2.189	0.099	2.289
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.056	0.000	0.057
annotate_eset_list	0.103	0.005	0.108
camera_score-methods	0.522	0.088	1.067
center_eSet	0.041	0.004	0.045
connectivity_score-methods	1.712	0.788	0.962
eSetOnDisk	0.006	0.000	0.007
eset_instances	0.087	0.012	0.098
featureScores-methods	0.192	0.074	0.713
fisher_score-methods	1.657	0.738	0.822
gCMAPData-dataset	0.149	0.069	0.691
geneIndex-methods	0.892	0.384	0.663
generate_gCMAP_NChannelSet	0.221	0.021	0.242
gsealm_jg_score-methods	1.799	0.833	0.938
gsealm_score-methods	2.401	0.126	3.548
induceCMAPCollection-methods	1.116	0.495	0.521
mapNmerge	0.000	0.000	0.001
memorize	0.009	0.001	0.010
mergeCMAPs	0.064	0.008	0.073
mgsa_score-methods	12.599	0.310	22.556
minSetSize-methods	1.009	0.485	0.630
mroast_score-methods	1.826	0.640	1.476
romer_score-methods	5.805	0.681	6.354
signedRankSumTest	0.002	0.000	0.002
splitPerturbations	0.053	0.004	0.057
wilcox_score-methods	1.558	0.720	0.841