BioC 2.14: CHECK report for gCMAP on zin2

Package: gCMAP

Version: 1.8.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.8.0.tar.gz

StartedAt: 2014-10-07 23:43:42 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:47:57 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 255.2 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/gCMAP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-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 ‘1.8.0’
* 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 ... [27s/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
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘BiocGenerics’ ‘Category’ ‘annotate’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GSEABase’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘GSEABase:::.showGeneSet’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘CMAPResults’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
eSetOnDisk: no visible global function definition for ‘BigMatrix’
* 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 ... [47s/43s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  12.724  0.212  12.819
romer_score-methods  8.041  0.124   7.935
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [34s/32s]
 [34s/32s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	0.812	0.164	0.766
CMAPResults-class	3.240	0.080	3.322
KEGG2cmap	0	0	0
SignedGeneSet-class	0.292	0.000	0.292
annotate_eset_list	0.112	0.004	0.116
camera_score-methods	0.460	0.060	0.771
center_eSet	0.032	0.000	0.032
connectivity_score-methods	0.920	0.416	0.609
eSetOnDisk	0.008	0.000	0.008
eset_instances	0.08	0.00	0.08
featureScores-methods	0.180	0.036	0.372
fisher_score-methods	0.936	0.272	0.470
gCMAPData-dataset	0.140	0.036	0.327
geneIndex-methods	0.412	0.152	0.329
generate_gCMAP_NChannelSet	0.212	0.012	0.225
gsealm_jg_score-methods	0.992	0.348	0.564
gsealm_score-methods	2.853	0.048	3.067
induceCMAPCollection-methods	0.452	0.104	0.282
mapNmerge	0.000	0.000	0.001
memorize	0.008	0.000	0.008
mergeCMAPs	0.104	0.000	0.103
mgsa_score-methods	12.724	0.212	12.819
minSetSize-methods	0.500	0.160	0.307
mroast_score-methods	0.888	0.156	0.834
romer_score-methods	8.041	0.124	7.935
signedRankSumTest	0.004	0.000	0.002
splitPerturbations	0.088	0.000	0.087
wilcox_score-methods	0.984	0.468	0.648