Back to Multiple platform build/check report for BioC 3.7 experimental data

CHECK report for ccTutorial on malbec2

This page was generated on 2018-10-16 14:17:09 -0400 (Tue, 16 Oct 2018).

Package 41/342HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ccTutorial 1.18.0
Joern Toedling
Snapshot Date: 2018-10-16 07:35:22 -0400 (Tue, 16 Oct 2018)
URL: https://git.bioconductor.org/packages/ccTutorial
Branch: RELEASE_3_7
Last Commit: 1ddd345
Last Changed Date: 2018-04-30 10:31:26 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ccTutorial
Version: 1.18.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ccTutorial.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ccTutorial_1.18.0.tar.gz
StartedAt: 2018-10-16 10:40:50 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 10:44:46 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 235.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ccTutorial.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ccTutorial.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ccTutorial_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/ccTutorial.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ccTutorial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ccTutorial’ version ‘1.18.0’
* 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 ‘ccTutorial’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 785.0Mb
  sub-directories of 1Mb or more:
    PairData       448.5Mb
    data            77.8Mb
    exonerateData  202.3Mb
    expression      49.9Mb
    vignettes        6.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  ‘Ringo’ ‘affy’ ‘topGO’
  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 ... OK
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
    user system elapsed
X 11.548  0.112  11.667
* 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-3.7-data-experiment/meat/ccTutorial.Rcheck/00check.log’
for details.



Installation output

ccTutorial.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ccTutorial
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ccTutorial’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (ccTutorial)

Tests output


Example timings

ccTutorial.Rcheck/ccTutorial-Ex.timings

nameusersystemelapsed
X11.548 0.11211.667
arrayGenesToProbeSets0.0360.0000.035
barreraExpressionX0.0800.0040.084
chersX0.5360.0080.542
mm9g2p0.7440.0120.755
mm9gene2GO0.0280.0000.028
mm9genes0.0760.0000.077
probeAnno000