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CHECK report for annotationTools on riesling1

This page was generated on 2020-10-18 12:33:08 -0400 (Sun, 18 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE annotationTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 65/1874HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotationTools 1.63.0
Alexandre Kuhn
Snapshot Date: 2020-10-17 14:41:49 -0400 (Sat, 17 Oct 2020)
URL: https://git.bioconductor.org/packages/annotationTools
Branch: master
Last Commit: 0a25929
Last Changed Date: 2020-04-27 14:14:46 -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
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annotationTools
Version: 1.63.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotationTools.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annotationTools_1.63.0.tar.gz
StartedAt: 2020-10-17 19:46:50 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 19:47:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 38.0 seconds
RetCode: 0
Status:  OK  
CheckDir: annotationTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotationTools.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annotationTools_1.63.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/annotationTools.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 'annotationTools/DESCRIPTION' ... OK
* this is package 'annotationTools' version '1.63.0'
* 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 'annotationTools' 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
** 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: OK


Installation output

annotationTools.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/annotationTools_1.63.0.tar.gz && rm -rf annotationTools.buildbin-libdir && mkdir annotationTools.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annotationTools.buildbin-libdir annotationTools_1.63.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL annotationTools_1.63.0.zip && rm annotationTools_1.63.0.tar.gz annotationTools_1.63.0.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  123k  100  123k    0     0  12.0M      0 --:--:-- --:--:-- --:--:-- 12.0M

install for i386

* installing *source* package 'annotationTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'annotationTools'
    finding HTML links ... done
    HG-U133_Plus_2_annot_part               html  
    HG-U133_Plus_2_ortholog_part            html  
    Mouse430_2_annot_part                   html  
    annot_HGU133A                           html  
    compactList                             html  
    gene_orthologs_part                     html  
    getANNOTATION                           html  
    getGENEID                               html  
    getGENEONTOLOGY                         html  
    getGENESYMBOL                           html  
    getGENETITLE                            html  
    getHOMOLOG                              html  
    getMULTIANNOTATION                      html  
    getOrthologousProbesets                 html  
    getPROBESET                             html  
    homologene_part                         html  
    listToCharacterVector                   html  
    ortho                                   html  
    ps2ps                                   html  
    table_human                             html  
    table_mouse                             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 'annotationTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotationTools' as annotationTools_1.63.0.zip
* DONE (annotationTools)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'annotationTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

annotationTools.Rcheck/examples_i386/annotationTools-Ex.timings

nameusersystemelapsed
compactList000
getANNOTATION0.020.000.02
getGENEID0.030.000.03
getGENEONTOLOGY0.010.000.02
getGENESYMBOL0.020.000.02
getGENETITLE0.030.000.03
getHOMOLOG0.010.000.01
getMULTIANNOTATION000
getOrthologousProbesets0.020.020.03
getPROBESET0.020.000.02
listToCharacterVector000
ps2ps000

annotationTools.Rcheck/examples_x64/annotationTools-Ex.timings

nameusersystemelapsed
compactList000
getANNOTATION000
getGENEID0.020.000.02
getGENEONTOLOGY0.010.000.01
getGENESYMBOL000
getGENETITLE0.020.000.01
getHOMOLOG0.010.000.02
getMULTIANNOTATION0.020.000.01
getOrthologousProbesets0.030.000.03
getPROBESET0.020.000.02
listToCharacterVector000
ps2ps000