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CHECK report for AffiXcan on tokay1

This page was generated on 2020-08-07 12:15:49 -0400 (Fri, 07 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: 2020-08-06 14:50:46 -0400 (Thu, 06 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
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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffiXcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AffiXcan_1.7.0.tar.gz
StartedAt: 2020-08-07 04:58:52 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 05:07:31 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 519.7 seconds
RetCode: 0
Status:  OK  
CheckDir: AffiXcan.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffiXcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AffiXcan_1.7.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AffiXcan.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
AffiXcan-package 3.63   0.18   75.87
affiXcanImpute   3.64   0.13   68.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
AffiXcan-package 4.96   0.04   83.25
affiXcanImpute   4.26   0.16   77.97
* 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
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/AffiXcan_1.7.0.tar.gz && rm -rf AffiXcan.buildbin-libdir && mkdir AffiXcan.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AffiXcan.buildbin-libdir AffiXcan_1.7.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AffiXcan_1.7.0.zip && rm AffiXcan_1.7.0.tar.gz AffiXcan_1.7.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1711k  100 1711k    0     0  29.3M      0 --:--:-- --:--:-- --:--:-- 32.1M

install for i386

* installing *source* package 'AffiXcan' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AffiXcan'
    finding HTML links ... done
    AffiXcan-package                        html  
    affiXcanBs                              html  
    affiXcanGReX                            html  
    affiXcanImpute                          html  
    affiXcanPca                             html  
    affiXcanPcs                             html  
    affiXcanTrain                           html  
    assoc2list                              html  
    computeBs                               html  
    computeCorrelation                      html  
    computeExpr                             html  
    computePca                              html  
    computePcs                              html  
    computeRSquared                         html  
    exprMatrix                              html  
    overlookRegions                         html  
    regionAssoc                             html  
    subsetKFold                             html  
    trainingCovariates                      html  
** 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

install for x64

* installing *source* package 'AffiXcan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffiXcan' as AffiXcan_1.7.0.zip
* DONE (AffiXcan)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AffiXcan' successfully unpacked and MD5 sums checked

Tests output


Example timings

AffiXcan.Rcheck/examples_i386/AffiXcan-Ex.timings

nameusersystemelapsed
AffiXcan-package 3.63 0.1875.87
affiXcanBs000
affiXcanGReX000
affiXcanImpute 3.64 0.1368.03
affiXcanPca000
affiXcanPcs000
affiXcanTrain000
assoc2list000
computeBs000
computeCorrelation0.020.000.01
computeExpr000
computePca000
computePcs000
computeRSquared000
exprMatrix0.010.000.02
overlookRegions0.000.010.01
regionAssoc000
subsetKFold000
trainingCovariates0.000.020.02

AffiXcan.Rcheck/examples_x64/AffiXcan-Ex.timings

nameusersystemelapsed
AffiXcan-package 4.96 0.0483.25
affiXcanBs000
affiXcanGReX0.020.000.01
affiXcanImpute 4.26 0.1677.97
affiXcanPca000
affiXcanPcs0.020.000.02
affiXcanTrain000
assoc2list000
computeBs000
computeCorrelation000
computeExpr000
computePca000
computePcs000
computeRSquared000
exprMatrix0.030.000.03
overlookRegions000
regionAssoc0.000.020.02
subsetKFold000
trainingCovariates0.000.010.02