Back to Multiple platform build/check report for BioC 3.8 experimental data

CHECK report for pumadata on malbec1

This page was generated on 2019-04-16 15:26:00 -0400 (Tue, 16 Apr 2019).

Package 265/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pumadata 2.18.0
Richard Pearson
Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019)
URL: https://git.bioconductor.org/packages/pumadata
Branch: RELEASE_3_8
Last Commit: 1bbdf0d
Last Changed Date: 2018-10-30 11:36:21 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: pumadata
Version: 2.18.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:pumadata.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings pumadata_2.18.0.tar.gz
StartedAt: 2019-04-16 13:59:47 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 14:01:58 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 131.9 seconds
RetCode: 0
Status:  OK 
CheckDir: pumadata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:pumadata.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings pumadata_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/pumadata.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pumadata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pumadata’ version ‘2.18.0’
* 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 ‘pumadata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 105.0Mb
  sub-directories of 1Mb or more:
    data  104.9Mb
* 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 ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘oligo’ ‘puma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘pumadata/R/zzz.R’:
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.onLoad: no visible global function definition for ‘addVigs2WinMenu’
Undefined global functions or variables:
  addVigs2WinMenu
* 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 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-data-experiment/meat/pumadata.Rcheck/00check.log’
for details.



Installation output

pumadata.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL pumadata
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘pumadata’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pumadata)

Tests output


Example timings

pumadata.Rcheck/pumadata-Ex.timings

nameusersystemelapsed
eset_estrogen_comb0.0920.0040.093
eset_estrogen_mmgmos0.0960.0040.102
eset_estrogen_pmmmgmos0.1120.0040.115
eset_estrogen_rma0.0240.0000.026
pumapca_estrogen0.0040.0000.008