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CHECK report for PAPi on malbec2

This page was generated on 2019-10-16 12:02:39 -0400 (Wed, 16 Oct 2019).

Package 1168/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAPi 1.24.0
Raphael Aggio
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PAPi
Branch: RELEASE_3_9
Last Commit: cfbc59e
Last Changed Date: 2019-05-02 11:53:42 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PAPi
Version: 1.24.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PAPi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PAPi_1.24.0.tar.gz
StartedAt: 2019-10-16 03:46:40 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:48:11 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 91.3 seconds
RetCode: 0
Status:  OK 
CheckDir: PAPi.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PAPi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PAPi_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PAPi.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAPi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PAPi’ version ‘1.24.0’
* 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 ‘PAPi’ 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
addKeggCodes: no visible global function definition for ‘read.csv’
addKeggCodes: no visible global function definition for ‘select.list’
addKeggCodes: no visible global function definition for ‘write.csv’
buildDatabase : apply_pb: no visible global function definition for
  ‘txtProgressBar’
buildDatabase : apply_pb : wrapper: no visible global function
  definition for ‘setTxtProgressBar’
buildDatabase: no visible global function definition for ‘write.csv’
papi: no visible global function definition for ‘read.csv’
papi: no visible global function definition for ‘select.list’
papi: no visible global function definition for ‘txtProgressBar’
papi: no visible global function definition for ‘setTxtProgressBar’
papi: no visible global function definition for ‘write.csv’
papiHtest : test.t : : no visible global function definition
  for ‘t.test’
papiHtest : anova.t : : no visible global function
  definition for ‘lm’
papiHtest : anova.t: no visible binding for global variable ‘anova’
papiHtest: no visible global function definition for ‘read.csv’
papiHtest: no visible global function definition for ‘p.adjust’
papiHtest: no visible global function definition for ‘write.csv’
papiLine: no visible global function definition for ‘read.csv’
papiLine: no visible global function definition for ‘colors’
papiLine: no visible global function definition for ‘png’
papiLine: no visible global function definition for ‘par’
papiLine: no visible global function definition for ‘plot’
papiLine: no visible global function definition for ‘points’
papiLine: no visible global function definition for ‘lines’
papiLine: no visible global function definition for ‘axis’
papiLine: no visible global function definition for ‘text’
papiLine: no visible global function definition for ‘legend’
papiLine: no visible global function definition for ‘graphics.off’
Undefined global functions or variables:
  anova axis colors graphics.off legend lines lm p.adjust par plot png
  points read.csv select.list setTxtProgressBar t.test text
  txtProgressBar write.csv
Consider adding
  importFrom("grDevices", "colors", "graphics.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "par", "plot",
             "points", "text")
  importFrom("stats", "anova", "lm", "p.adjust", "t.test")
  importFrom("utils", "read.csv", "select.list", "setTxtProgressBar",
             "txtProgressBar", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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-3.9-bioc/meat/PAPi.Rcheck/00check.log’
for details.



Installation output

PAPi.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PAPi
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘PAPi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘PAPiPackage.Rnw’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PAPi)

Tests output


Example timings

PAPi.Rcheck/PAPi-Ex.timings

nameusersystemelapsed
PAPi-package0.0020.0010.002
addKeggCodes0.0070.0000.007
buildDatabase000
keggLibrary0.0130.0000.013
metabolomicsData0.0020.0000.002
papi0.0000.0000.001
papiData0.0020.0000.002
papiHtest0.0150.0000.014
papiLine0.0000.0000.001
papiResults0.0030.0000.004