BioC 3.3: CHECK report for cogena on linux2.bioconductor.org

Package: cogena

Version: 1.2.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cogena_1.2.0.tar.gz

StartedAt: 2015-10-27 02:51:47 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:55:07 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 200.0 seconds

RetCode: 0

Status:  OK

CheckDir: cogena.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cogena_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/cogena.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogena/DESCRIPTION’ ... OK
* this is package ‘cogena’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘cogena’ can be installed ... [6s/6s] OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   3.1Mb
* 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 loading without being on the library search path ... OK
* checking 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/128s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cogena_package 5.881  0.311  73.851
clEnrich_one   4.593  0.085  11.287
clEnrich       3.438  0.090  14.042
upDownGene     3.397  0.110  14.798
clusterMethods 1.691  0.027   8.355
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/cogena.Rcheck/00check.log’
for details.

* installing *source* package ‘cogena’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘cogena’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cogena)

name	user	system	elapsed
PEI	1.067	0.016	1.083
clEnrich	3.438	0.090	14.042
clEnrich_one	4.593	0.085	11.287
clusterMethods	1.691	0.027	8.355
coExp	0.003	0.000	0.003
cogena_package	5.881	0.311	73.851
corInCluster	0.002	0.000	0.001
enrichment	0.002	0.000	0.002
gene2set	0.069	0.000	0.070
geneExpInCluster	0.002	0.000	0.002
geneInCluster	0.002	0.000	0.002
geneclusters	0.000	0.000	0.001
gmt2list	0.031	0.000	0.030
heatmapCluster	0.002	0.000	0.002
heatmapCmap	0.002	0.000	0.002
heatmapPEI	0.002	0.000	0.002
mat	0.001	0.000	0.000
nClusters	0.001	0.000	0.001
show	0.001	0.000	0.001
sota	2.034	0.000	2.048
summary	0.001	0.000	0.001
upDownGene	3.397	0.110	14.798