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CHECK report for MAQCsubset on malbec2

This page was generated on 2018-10-16 14:16:51 -0400 (Tue, 16 Oct 2018).

Package 189/342HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAQCsubset 1.18.0
VJ Carey
Snapshot Date: 2018-10-16 07:35:22 -0400 (Tue, 16 Oct 2018)
URL: https://git.bioconductor.org/packages/MAQCsubset
Branch: RELEASE_3_7
Last Commit: d40614d
Last Changed Date: 2018-04-30 10:31:25 -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: MAQCsubset
Version: 1.18.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MAQCsubset.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MAQCsubset_1.18.0.tar.gz
StartedAt: 2018-10-16 11:08:13 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 11:11:55 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 222.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MAQCsubset.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:MAQCsubset.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MAQCsubset_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/MAQCsubset.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 ‘MAQCsubset/DESCRIPTION’ ... OK
* this is package ‘MAQCsubset’ 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 ‘MAQCsubset’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 64.4Mb
  sub-directories of 1Mb or more:
    data  64.1Mb
* 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 ‘genefilter’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘lumi’ ‘methods’
  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
proboscis: no visible global function definition for ‘rowttests’
proboscis: no visible global function definition for ‘exprs’
plot,proboStruct-ANY: no visible global function definition for ‘plot’
Undefined global functions or variables:
  exprs plot rowttests
Consider adding
  importFrom("graphics", "plot")
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 ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'lumi'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/MAQCsubset.Rcheck/00check.log’
for details.



Installation output

MAQCsubset.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL MAQCsubset
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘MAQCsubset’ ...
** 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 (MAQCsubset)

Tests output


Example timings

MAQCsubset.Rcheck/MAQCsubset-Ex.timings

nameusersystemelapsed
MAQCsubset0.8080.0240.833
gehMAQCsubDef0.3640.0080.372
gnfCerebHi0.0080.0000.008
proboStruct-class1.7840.0081.792
proboscis1.0000.0241.027