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CHECK report for GSALightning on tokay2

This page was generated on 2020-10-17 11:56:47 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GSALightning PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 781/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSALightning 1.16.0
Billy Heung Wing Chang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GSALightning
Branch: RELEASE_3_11
Last Commit: 78ba9ff
Last Changed Date: 2020-04-27 14:53:36 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSALightning
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSALightning.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GSALightning_1.16.0.tar.gz
StartedAt: 2020-10-17 04:45:21 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:47:29 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 128.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GSALightning.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSALightning.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GSALightning_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GSALightning.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSALightning/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSALightning' version '1.16.0'
* 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 whether package 'GSALightning' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/GSALightning.Rcheck/00check.log'
for details.



Installation output

GSALightning.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GSALightning_1.16.0.tar.gz && rm -rf GSALightning.buildbin-libdir && mkdir GSALightning.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSALightning.buildbin-libdir GSALightning_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GSALightning_1.16.0.zip && rm GSALightning_1.16.0.tar.gz GSALightning_1.16.0.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 4013k  100 4013k    0     0  38.3M      0 --:--:-- --:--:-- --:--:-- 41.2M

install for i386

* installing *source* package 'GSALightning' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSALightning'
    finding HTML links ... done
    GSALight                                html  
    GSALightning-package                    html  
    expression                              html  
    permTestLight                           html  
    sampleInfo                              html  
    targetGenes                             html  
    wilcoxTest                              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 'GSALightning' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSALightning' as GSALightning_1.16.0.zip
* DONE (GSALightning)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GSALightning' successfully unpacked and MD5 sums checked

Tests output


Example timings

GSALightning.Rcheck/examples_i386/GSALightning-Ex.timings

nameusersystemelapsed
GSALight0.770.120.89
expression0.390.020.40
permTestLight0.260.050.31
sampleInfo0.020.000.02
targetGenes0.340.000.34
wilcoxTest0.190.000.19

GSALightning.Rcheck/examples_x64/GSALightning-Ex.timings

nameusersystemelapsed
GSALight1.00.11.1
expression0.310.040.35
permTestLight0.340.110.45
sampleInfo0.020.000.02
targetGenes0.480.000.48
wilcoxTest0.280.020.30