Package: gCMAP

Version: 1.3.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.3.5.tar.gz

StartedAt: 2013-03-25 02:33:40 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:40:00 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 380.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gCMAP.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/gCMAP.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gCMAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gCMAP' version '1.3.5'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'gCMAP' can be installed ... [40s/40s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 examples ... [96s/70s] WARNING
Found the following significant warnings:

  Warning: '.path.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                       user system elapsed
mgsa_score-methods   35.384  1.101  16.138
romer_score-methods  15.469  0.586  15.635
gsealm_score-methods  5.460  0.419   5.783
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [63s/52s]
 [63s/52s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
   'diffExprAnalysis.Rnw' 
   'gCMAP.Rnw' 
** testing if installed package can be loaded
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	1.319	0.407	1.430
CMAPResults-class	4.581	0.213	4.802
KEGG2cmap	0.007	0.008	0.015
SignedGeneSet-class	0.081	0.010	0.090
annotate_eset_list	0.149	0.013	0.164
camera_score-methods	0.854	0.269	1.215
center_eSet	0.021	0.012	0.033
connectivity_score-methods	1.081	0.852	1.033
eSetOnDisk	0.782	0.168	0.955
eset_instances	0.113	0.017	0.132
featureScores-methods	0.290	0.162	0.718
fisher_score-methods	1.238	0.764	0.911
gCMAPData-dataset	0.444	0.283	0.626
geneIndex-methods	0.379	0.203	0.553
generate_gCMAP_NChannelSet	0.279	0.058	0.342
gsealm_jg_score-methods	1.339	0.909	1.141
gsealm_score-methods	5.460	0.419	5.783
induceCMAPCollection-methods	0.333	0.190	0.491
mapNmerge	0.009	0.010	0.019
memorize	0.925	0.188	1.119
mergeCMAPs	0.205	0.023	0.229
mgsa_score-methods	35.384	1.101	16.138
minSetSize-methods	0.394	0.229	0.613
mroast_score-methods	2.036	0.742	2.105
romer_score-methods	15.469	0.586	15.635
signedRankSumTest	0.015	0.022	0.042
splitPerturbations	0.121	0.023	0.145
wilcox_score-methods	1.065	0.997	1.174