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CHECK report for KEGGprofile on tokay2

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

TO THE DEVELOPERS/MAINTAINERS OF THE KEGGprofile PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 921/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGprofile 1.30.0
Shilin Zhao
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/KEGGprofile
Branch: RELEASE_3_11
Last Commit: 1a4127f
Last Changed Date: 2020-04-27 14:30:12 -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: KEGGprofile
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGprofile.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings KEGGprofile_1.30.0.tar.gz
StartedAt: 2020-10-17 05:27:32 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:33:03 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 330.7 seconds
RetCode: 0
Status:  OK  
CheckDir: KEGGprofile.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:KEGGprofile.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings KEGGprofile_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/KEGGprofile.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 'KEGGprofile/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGprofile' version '1.30.0'
* 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 'KEGGprofile' 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
convertId         12.42   0.07   16.19
plot_pathway       6.92   0.64    7.56
download_KEGGfile  0.58   0.33    7.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
plot_pathway 8.47   0.61    9.08
convertId    8.47   0.01   12.08
* 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: OK


Installation output

KEGGprofile.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/KEGGprofile_1.30.0.tar.gz && rm -rf KEGGprofile.buildbin-libdir && mkdir KEGGprofile.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGprofile.buildbin-libdir KEGGprofile_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL KEGGprofile_1.30.0.zip && rm KEGGprofile_1.30.0.tar.gz KEGGprofile_1.30.0.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  313k  100  313k    0     0  4825k      0 --:--:-- --:--:-- --:--:-- 5409k

install for i386

* installing *source* package 'KEGGprofile' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KEGGprofile'
    finding HTML links ... done
    KEGGprofile-package                     html  
    col_by_value                            html  
    convertId                               html  
    download_KEGGfile                       html  
    download_latest_pathway                 html  
    find_enriched_pathway                   html  
    newIdMatrix                             html  
    parse_XMLfile                           html  
    pho_sites_count                         html  
    plot_pathway                            html  
    plot_pathway_cor                        html  
    plot_pathway_overall                    html  
    plot_profile                            html  
    pro_pho_expr                            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 'KEGGprofile' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGprofile' as KEGGprofile_1.30.0.zip
* DONE (KEGGprofile)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'KEGGprofile' successfully unpacked and MD5 sums checked

Tests output


Example timings

KEGGprofile.Rcheck/examples_i386/KEGGprofile-Ex.timings

nameusersystemelapsed
col_by_value0.030.000.03
convertId12.42 0.0716.19
download_KEGGfile0.580.337.91
download_latest_pathway000
find_enriched_pathway3.480.134.42
newIdMatrix000
parse_XMLfile0.050.000.05
plot_pathway6.920.647.56
plot_pathway_cor3.370.223.59
plot_pathway_overall3.290.173.49
plot_profile1.420.201.62

KEGGprofile.Rcheck/examples_x64/KEGGprofile-Ex.timings

nameusersystemelapsed
col_by_value0.020.000.02
convertId 8.47 0.0112.08
download_KEGGfile0.590.113.18
download_latest_pathway000
find_enriched_pathway3.560.033.60
newIdMatrix000
parse_XMLfile0.060.000.06
plot_pathway8.470.619.08
plot_pathway_cor3.890.134.22
plot_pathway_overall2.990.033.01
plot_profile0.920.151.08