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CHECK report for AffiXcan on merida1

This page was generated on 2020-08-09 12:40:37 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AffiXcan PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 21/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffiXcan 1.7.0
Alessandro Lussana
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/AffiXcan
Branch: master
Last Commit: b51795e
Last Changed Date: 2020-04-27 15:20:00 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AffiXcan
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2020-08-09 03:58:14 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 04:01:54 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 220.6 seconds
RetCode: 0
Status:  OK 
CheckDir: AffiXcan.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AffiXcan.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffiXcan/DESCRIPTION’ ... OK
* this is package ‘AffiXcan’ version ‘1.7.0’
* 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’
computeBs: no visible global function definition for ‘pf’
computeCorrelation: no visible global function definition for ‘cor’
computeCorrelation: no visible global function definition for
  ‘cor.test’
computePca: no visible global function definition for ‘var’
computePca: no visible global function definition for ‘prcomp’
computeRSquared: no visible binding for global variable ‘exprMatrix’
Undefined global functions or variables:
  V1 anova cor cor.test exprMatrix lm p.adjust pf prcomp setNames var
Consider adding
  importFrom("stats", "anova", "cor", "cor.test", "lm", "p.adjust", "pf",
             "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 (user + system) or elapsed time > 5s
                  user system elapsed
AffiXcan-package 4.499   0.98   3.599
* 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-3.12-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/4.0/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-package4.4990.9803.599
affiXcanBs0.0040.0010.004
affiXcanGReX0.0030.0000.003
affiXcanImpute3.1820.7432.212
affiXcanPca0.0020.0010.003
affiXcanPcs0.0030.0010.004
affiXcanTrain0.0010.0010.002
assoc2list0.0000.0000.001
computeBs0.0100.0010.011
computeCorrelation0.0030.0000.003
computeExpr0.0030.0000.004
computePca0.0030.0000.004
computePcs0.0040.0010.004
computeRSquared0.0020.0000.002
exprMatrix0.0140.0040.018
overlookRegions0.0010.0010.001
regionAssoc0.0070.0040.011
subsetKFold0.0010.0000.001
trainingCovariates0.0050.0030.008