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BioC 3.3: CHECK report for clipper on zin2

This page was generated on 2016-10-13 12:43:41 -0700 (Thu, 13 Oct 2016).

Package 196/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.12.0
Paolo Martini
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/clipper
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clipper
Version: 1.12.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings clipper_1.12.0.tar.gz
StartedAt: 2016-10-13 00:34:19 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 00:38:04 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 224.8 seconds
RetCode: 0
Status:  OK 
CheckDir: clipper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings clipper_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/clipper.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.12.0’
* 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 ‘clipper’ 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 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
cliqueMeanTest : <anonymous>: no visible global function definition for
  ‘t.test’
cliqueMixedTest : <anonymous>: no visible global function definition
  for ‘t.test’
cliquePairedTest : <anonymous>: no visible global function definition
  for ‘t.test’
cliquePairedTest : <anonymous>: no visible global function definition
  for ‘pf’
cliqueParamTest: no visible global function definition for ‘pchisq’
estimateExprCov: no visible global function definition for ‘cov’
hote4mean: no visible global function definition for ‘cov’
hote4mean: no visible global function definition for ‘pf’
prunePaths: no visible global function definition for ‘hclust’
prunePaths: no visible global function definition for ‘as.dist’
prunePaths: no visible global function definition for ‘pdf’
prunePaths: no visible global function definition for ‘dev.off’
prunePaths: no visible global function definition for ‘cutree’
runPathwayVar: no visible global function definition for ‘qchisq’
runPathwayVar: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  as.dist cov cutree dev.off hclust pchisq pdf pf qchisq t.test
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "as.dist", "cov", "cutree", "hclust", "pchisq",
             "pf", "qchisq", "t.test")
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 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
clipperAllRoots 10.610  0.047  10.794
pathwayTest     10.032  0.019  10.272
clipper          5.295  0.088   5.651
* 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/clipper.Rcheck/00check.log’
for details.


clipper.Rcheck/00install.out:

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

clipper.Rcheck/clipper-Ex.timings:

nameusersystemelapsed
clipper5.2950.0885.651
clipperAllRoots10.610 0.04710.794
cliqueMeanTest2.9560.0163.015
cliqueMixedTest2.9040.0362.991
cliquePairedTest3.3010.0243.355
cliqueVarianceTest2.7740.0162.808
deleteEdge0.1470.0000.150
easyClip2.9220.0202.986
getGraphEntryGenes0.2170.0000.226
getJunctionTreePaths0.2120.0040.221
nameCliques0.0010.0000.001
pathwayTest10.032 0.01910.272
plotInCytoscape0.0010.0000.001
prunePaths0.0020.0040.003