BioC 3.2: CHECK report for pwOmics on perceval

Package: pwOmics

Version: 1.1.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pwOmics_1.1.13.tar.gz

StartedAt: 2015-08-24 04:07:55 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:11:06 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 191.1 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_1.1.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/pwOmics.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.1.13’
* 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 ... [15s/15s] 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 ... [27s/28s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
readTFdata 14.508  1.403  16.807
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [8s/8s] 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	0.075	0.012	0.087
consDynamicNet	0.062	0.005	0.067
enrichPWs	0.061	0.007	0.067
enrichTFs	0.071	0.006	0.078
getBiopaxModel	0.063	0.005	0.068
getDS_PWs	0.064	0.004	0.068
getDS_TFs	0.072	0.004	0.076
getDS_TGs	0.062	0.005	0.067
getGenesIntersection	0.071	0.004	0.074
getOmicsDataset	0.150	0.073	0.224
getOmicsTimepoints	0.067	0.004	0.072
getOmicsallGeneIDs	1.142	0.205	1.348
getOmicsallProteinIDs	0.092	0.015	0.108
getProteinIntersection	0.062	0.005	0.068
getTFIntersection	0.067	0.006	0.072
getUS_PWs	0.071	0.006	0.076
getUS_TFs	0.072	0.005	0.076
getUS_regulators	0.063	0.004	0.067
gettpIntersection	0.070	0.005	0.075
identifyPWTFTGs	0.068	0.005	0.074
identifyPWs	0.062	0.004	0.067
identifyRsofTFs	0.062	0.004	0.066
identifyTFs	0.069	0.004	0.073
plotConsDynNet	0.068	0.004	0.073
plotConsensusGraph	0.064	0.004	0.068
plotTimeProfileClusters	0.067	0.005	0.072
readOmics	0.069	0.005	0.073
readPWdata	0.064	0.005	0.068
readTFdata	14.508	1.403	16.807
staticConsensusNet	0.071	0.018	0.089