BioC 3.2: CHECK report for gCMAP on zin1

Package: gCMAP

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.14.0.tar.gz

StartedAt: 2016-04-23 00:51:46 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:54:56 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 190.1 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/gCMAP.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.14.0’
* 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 ... [19s/19s] 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 ... [48s/33s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  15.705  0.251    6.03
romer_score-methods  8.232  0.263    8.00
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [33s/26s]
 [33s/26s] 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-3.2-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	0.892	0.167	0.696
CMAPResults-class	2.353	0.048	2.496
KEGG2cmap	0.000	0.004	0.000
SignedGeneSet-class	0.036	0.000	0.039
annotate_eset_list	0.083	0.000	0.083
camera_score-methods	0.413	0.052	0.722
center_eSet	0.026	0.000	0.026
connectivity_score-methods	1.160	0.414	0.619
eSetOnDisk	0.003	0.004	0.005
eset_instances	0.063	0.008	0.072
featureScores-methods	0.123	0.039	0.410
fisher_score-methods	1.142	0.349	0.512
gCMAPData-dataset	0.104	0.040	0.399
geneIndex-methods	0.611	0.125	0.381
generate_gCMAP_NChannelSet	0.170	0.016	0.185
gsealm_jg_score-methods	1.228	0.343	0.559
gsealm_score-methods	2.370	0.068	2.702
induceCMAPCollection-methods	0.559	0.172	0.380
mapNmerge	0.001	0.000	0.001
memorize	0.004	0.000	0.004
mergeCMAPs	0.076	0.012	0.088
mgsa_score-methods	15.705	0.251	6.030
minSetSize-methods	0.727	0.160	0.451
mroast_score-methods	1.302	0.268	1.206
romer_score-methods	8.232	0.263	8.000
signedRankSumTest	0.002	0.000	0.003
splitPerturbations	0.078	0.000	0.078
wilcox_score-methods	1.282	0.496	0.761