BioC 3.1: CHECK report for pwOmics on zin2

Package: pwOmics

Version: 1.0.2

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings pwOmics_1.0.2.tar.gz

StartedAt: 2015-10-09 04:33:29 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:35:27 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 118.8 seconds

RetCode: 0

Status:  OK

CheckDir: pwOmics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings pwOmics_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/pwOmics.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.2’
* 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 ... [9s/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 ... NOTE
SteinerTree_cons: no visible binding for global variable ‘igraph’
* 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 ... [19s/20s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
readTFdata 11.708  0.462  13.347
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [5s/5s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/pwOmics.Rcheck/00check.log’
for details.

* installing *source* package ‘pwOmics’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (pwOmics)

name	user	system	elapsed
clusterTimeProfiles	0.058	0.000	0.057
dynamicConsensusNet	0.057	0.000	0.058
enrichPWs	0.047	0.000	0.049
enrichTFs	0.040	0.008	0.048
getBiopaxModel	0.051	0.000	0.052
getDS_PWs	0.049	0.000	0.048
getDS_TFs	0.047	0.004	0.052
getDS_TGs	0.049	0.000	0.048
getGenesIntersection	0.048	0.000	0.049
getOmicsDataset	0.087	0.032	0.119
getOmicsTimepoints	0.048	0.000	0.048
getOmicsallGeneIDs	0.278	0.112	0.390
getOmicsallProteinIDs	0.246	0.008	0.254
getProteinIntersection	0.055	0.000	0.055
getTFIntersection	0.052	0.004	0.056
getUS_PWs	0.054	0.000	0.054
getUS_TFs	0.055	0.000	0.058
getUS_regulators	0.053	0.000	0.053
gettpIntersection	0.05	0.00	0.05
identifyPWTFTGs	0.047	0.000	0.048
identifyPWs	0.048	0.000	0.047
identifyRsofTFs	0.050	0.000	0.051
identifyTFs	0.044	0.004	0.048
plotConsensusGraph	0.049	0.000	0.048
plotTimeProfileClusters	0.048	0.000	0.049
plotdynConsensusNet	0.052	0.000	0.052
readOmics	0.049	0.000	0.049
readPWdata	0.048	0.000	0.048
readTFdata	11.708	0.462	13.347
staticConsensusNet	0.05	0.00	0.05