BioC 2.13: CHECK report for gCMAP on zin1

Package: gCMAP

Version: 1.6.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.6.0.tar.gz

StartedAt: 2014-04-05 01:16:52 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:21:20 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 268.1 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/gCMAP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘diffExprAnalysis.Rnw’, ‘gCMAP.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [50s/48s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  12.765  0.164  12.800
romer_score-methods 10.136  0.140  10.185
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [38s/36s]
 [39s/36s] 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-2.13-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	0.788	0.128	0.690
CMAPResults-class	3.432	0.088	3.655
KEGG2cmap	0.004	0.000	0.004
SignedGeneSet-class	0.064	0.000	0.061
annotate_eset_list	0.124	0.000	0.122
camera_score-methods	0.484	0.032	0.753
center_eSet	0.032	0.004	0.035
connectivity_score-methods	0.992	0.456	0.657
eSetOnDisk	0.984	0.052	1.067
eset_instances	0.080	0.004	0.084
featureScores-methods	0.236	0.036	0.343
fisher_score-methods	0.640	0.208	0.429
gCMAPData-dataset	0.164	0.044	0.440
geneIndex-methods	0.364	0.076	0.260
generate_gCMAP_NChannelSet	0.224	0.008	0.234
gsealm_jg_score-methods	0.772	0.236	0.501
gsealm_score-methods	2.997	0.076	3.145
induceCMAPCollection-methods	0.332	0.068	0.229
mapNmerge	0.000	0.004	0.005
memorize	0.728	0.060	0.789
mergeCMAPs	0.112	0.000	0.110
mgsa_score-methods	12.765	0.164	12.800
minSetSize-methods	0.288	0.108	0.239
mroast_score-methods	1.148	0.096	1.091
romer_score-methods	10.136	0.140	10.185
signedRankSumTest	0.004	0.004	0.007
splitPerturbations	0.092	0.000	0.093
wilcox_score-methods	0.704	0.348	0.544