BioC 3.3: CHECK report for pwOmics on morelia

Package: pwOmics

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pwOmics_1.3.0.tar.gz

StartedAt: 2015-10-22 09:57:06 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 09:59:05 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 119.5 seconds

RetCode: 0

Status:  OK

CheckDir: pwOmics.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pwOmics_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pwOmics.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pwOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pwOmics’ version ‘1.3.0’
* 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 ‘pwOmics’ can be installed ... [8s/9s] 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/19s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
readTFdata 11.397   0.58  13.131
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [4s/4s] 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: OK

* installing *source* package ‘pwOmics’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pwOmics)

name	user	system	elapsed
clusterTimeProfiles	0.048	0.003	0.051
consDynamicNet	0.041	0.003	0.044
enrichPWs	0.048	0.002	0.050
enrichTFs	0.040	0.003	0.043
getBiopaxModel	0.040	0.003	0.043
getDS_PWs	0.043	0.003	0.045
getDS_TFs	0.039	0.002	0.042
getDS_TGs	0.042	0.002	0.044
getGenesIntersection	0.044	0.002	0.046
getOmicsDataset	0.090	0.037	0.128
getOmicsTimepoints	0.178	0.003	0.181
getOmicsallGeneIDs	0.454	0.115	0.568
getOmicsallProteinIDs	0.084	0.009	0.093
getProteinIntersection	0.052	0.002	0.055
getTFIntersection	0.044	0.002	0.046
getUS_PWs	0.040	0.002	0.043
getUS_TFs	0.053	0.002	0.055
getUS_regulators	0.046	0.002	0.049
gettpIntersection	0.040	0.002	0.042
identifyPWTFTGs	0.040	0.002	0.042
identifyPWs	0.042	0.002	0.044
identifyRsofTFs	0.044	0.002	0.046
identifyTFs	0.040	0.002	0.044
plotConsDynNet	0.041	0.002	0.043
plotConsensusGraph	0.045	0.003	0.047
plotTimeProfileClusters	0.067	0.003	0.071
readOmics	0.063	0.003	0.067
readPWdata	0.063	0.003	0.066
readTFdata	11.397	0.580	13.131
staticConsensusNet	0.042	0.002	0.045