BioC 3.3: CHECK report for pwOmics on oaxaca

Package: pwOmics

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pwOmics_1.4.0.tar.gz

StartedAt: 2016-10-13 05:18:53 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:21:41 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 168.4 seconds

RetCode: 0

Status:  OK

CheckDir: pwOmics.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pwOmics_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pwOmics.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.4.0’
* 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 ... 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 global function definition for ‘na.omit’
clusterTimeProfiles: no visible global function definition for
  ‘na.omit’
consDynamicNet: no visible global function definition for ‘ts’
enrichPWs: no visible global function definition for ‘fisher.test’
enrichPWs: no visible global function definition for ‘p.adjust’
enrichTFs: no visible global function definition for ‘fisher.test’
enrichTFs: no visible global function definition for ‘p.adjust’
getAliasfromSTRINGIDs: no visible global function definition for
  ‘na.omit’
getConsensusSTRINGIDs: no visible global function definition for
  ‘na.omit’
getFCsplines: no visible global function definition for ‘smooth.spline’
getOmicsDataset: no visible global function definition for ‘write.csv’
identifyRsofTFs: no visible global function definition for ‘na.omit’
plotConsDynNet: no visible global function definition for ‘pdf’
plotConsDynNet: no visible global function definition for ‘qnorm’
plotConsDynNet: no visible global function definition for ‘dev.off’
plotConsensusGraph: no visible global function definition for ‘pdf’
plotConsensusGraph: no visible global function definition for ‘dev.off’
plotConsensusProfiles: no visible global function definition for ‘pdf’
plotConsensusProfiles: no visible global function definition for
  ‘dev.off’
plotTimeProfileClusters: no visible global function definition for
  ‘pdf’
plotTimeProfileClusters: no visible global function definition for
  ‘rainbow’
plotTimeProfileClusters: no visible global function definition for
  ‘dev.off’
predictFCvals: no visible global function definition for ‘predict’
readTFtargets: no visible global function definition for ‘read.delim’
selectPWsofTFs: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  dev.off fisher.test na.omit p.adjust pdf predict qnorm rainbow
  read.delim smooth.spline ts write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("stats", "fisher.test", "na.omit", "p.adjust", "predict",
             "qnorm", "smooth.spline", "ts")
  importFrom("utils", "read.delim", "write.csv")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
readTFdata 19.219   0.94  20.874
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.3-bioc/meat/pwOmics.Rcheck/00check.log’
for details.

* 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	0.100	0.012	0.112
consDynamicNet	0.046	0.004	0.050
enrichPWs	0.054	0.004	0.058
enrichTFs	0.063	0.004	0.067
getBiopaxModel	0.063	0.005	0.068
getDS_PWs	0.060	0.003	0.064
getDS_TFs	0.062	0.005	0.067
getDS_TGs	0.067	0.005	0.071
getGenesIntersection	0.058	0.004	0.062
getOmicsDataset	0.136	0.059	0.194
getOmicsTimepoints	0.074	0.004	0.079
getOmicsallGeneIDs	0.591	0.159	0.750
getOmicsallProteinIDs	0.086	0.013	0.099
getProteinIntersection	0.073	0.004	0.077
getTFIntersection	0.244	0.005	0.249
getUS_PWs	0.057	0.004	0.061
getUS_TFs	0.047	0.005	0.051
getUS_regulators	0.056	0.005	0.062
gettpIntersection	0.069	0.006	0.076
identifyPWTFTGs	0.063	0.005	0.068
identifyPWs	0.063	0.005	0.068
identifyRsofTFs	0.062	0.006	0.068
identifyTFs	0.061	0.005	0.067
plotConsDynNet	0.059	0.004	0.064
plotConsensusGraph	0.060	0.004	0.064
plotConsensusProfiles	0.059	0.005	0.064
plotTimeProfileClusters	0.062	0.005	0.068
readOmics	0.060	0.005	0.065
readPWdata	0.053	0.005	0.058
readTFdata	19.219	0.940	20.874
staticConsensusNet	0.094	0.012	0.106