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CHECK report for AffiXcan on celaya2

This page was generated on 2019-04-09 13:21:10 -0400 (Tue, 09 Apr 2019).

Package 20/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffiXcan 1.1.3
Alessandro Lussana
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/AffiXcan
Branch: master
Last Commit: 7bc0abc
Last Changed Date: 2019-03-05 16:10:35 -0400 (Tue, 05 Mar 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: AffiXcan
Version: 1.1.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AffiXcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffiXcan_1.1.3.tar.gz
StartedAt: 2019-04-08 23:44:29 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:48:31 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 241.9 seconds
RetCode: 0
Status:  OK 
CheckDir: AffiXcan.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AffiXcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffiXcan_1.1.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AffiXcan.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffiXcan/DESCRIPTION’ ... OK
* this is package ‘AffiXcan’ version ‘1.1.3’
* package encoding: UTF-8
* 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 ‘AffiXcan’ 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
affiXcanBs: no visible global function definition for ‘p.adjust’
affiXcanPcs: no visible global function definition for ‘setNames’
computeBs: no visible binding for global variable ‘V1’
computeBs: no visible global function definition for ‘lm’
computeBs: no visible global function definition for ‘anova’
computePca: no visible global function definition for ‘var’
computePca: no visible global function definition for ‘prcomp’
Undefined global functions or variables:
  V1 anova lm p.adjust prcomp setNames var
Consider adding
  importFrom("stats", "anova", "lm", "p.adjust", "prcomp", "setNames",
             "var")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
AffiXcan-package 12.176 13.373  14.742
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/AffiXcan.Rcheck/00check.log’
for details.



Installation output

AffiXcan.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AffiXcan
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘AffiXcan’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (AffiXcan)

Tests output


Example timings

AffiXcan.Rcheck/AffiXcan-Ex.timings

nameusersystemelapsed
AffiXcan-package12.17613.37314.742
affiXcanBs0.0030.0010.004
affiXcanGReX0.0050.0010.006
affiXcanImpute0.0040.0000.004
affiXcanPca0.0010.0000.001
affiXcanPcs0.0040.0000.005
affiXcanTrain0.0020.0000.003
assoc2list0.0010.0000.002
computeBs0.0040.0010.005
computeExpr0.0050.0000.006
computePca0.0010.0000.001
computePcs0.0030.0000.003
exprMatrix0.0180.0050.024
overlookRegions000
regionAssoc0.0090.0050.013
trainingCovariates0.0050.0030.008