BioC 3.1: CHECK report for pwOmics on petty

Package: pwOmics

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pwOmics_1.0.2.tar.gz

StartedAt: 2015-10-09 01:16:59 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:20:53 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 233.8 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_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.0.2’
* 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 ... [19s/19s] 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 ... [37s/43s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
readTFdata 21.958  2.189  29.467
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [9s/9s] 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
  ‘/Users/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	0.100	0.016	0.116
dynamicConsensusNet	0.108	0.009	0.117
enrichPWs	0.097	0.011	0.108
enrichTFs	0.115	0.011	0.125
getBiopaxModel	0.103	0.009	0.112
getDS_PWs	0.093	0.011	0.104
getDS_TFs	0.108	0.009	0.118
getDS_TGs	0.107	0.008	0.115
getGenesIntersection	0.098	0.008	0.107
getOmicsDataset	0.220	0.097	0.411
getOmicsTimepoints	0.107	0.008	0.116
getOmicsallGeneIDs	1.163	0.246	1.562
getOmicsallProteinIDs	0.149	0.024	0.172
getProteinIntersection	0.113	0.009	0.121
getTFIntersection	0.085	0.008	0.093
getUS_PWs	0.118	0.008	0.127
getUS_TFs	0.104	0.009	0.125
getUS_regulators	0.102	0.010	0.112
gettpIntersection	0.37	0.01	0.38
identifyPWTFTGs	0.071	0.008	0.078
identifyPWs	0.099	0.008	0.107
identifyRsofTFs	0.096	0.010	0.105
identifyTFs	0.090	0.009	0.099
plotConsensusGraph	0.093	0.009	0.102
plotTimeProfileClusters	0.071	0.007	0.078
plotdynConsensusNet	0.074	0.007	0.080
readOmics	0.087	0.009	0.095
readPWdata	0.076	0.007	0.084
readTFdata	21.958	2.189	29.467
staticConsensusNet	0.091	0.004	0.095