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CHECK report for TargetScoreData on riesling1

This page was generated on 2021-01-14 15:59:12 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE TargetScoreData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 351/385HostnameOS / ArchINSTALLBUILDCHECK
TargetScoreData 1.27.0
Yue Li
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/TargetScoreData
Branch: master
Last Commit: bb9c487
Last Changed Date: 2020-10-27 10:04:44 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: TargetScoreData
Version: 1.27.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TargetScoreData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TargetScoreData_1.27.0.tar.gz
StartedAt: 2021-01-14 11:44:01 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:44:30 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 29.4 seconds
RetCode: 0
Status:  OK  
CheckDir: TargetScoreData.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TargetScoreData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TargetScoreData_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/TargetScoreData.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TargetScoreData/DESCRIPTION' ... OK
* this is package 'TargetScoreData' version '1.27.0'
* 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 'TargetScoreData' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 227.4Mb
  sub-directories of 1Mb or more:
    extdata  227.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
get_miRNA_family_info: no visible global function definition for
  'read.delim'
get_validated_targets: no visible global function definition for
  'read.xls'
Undefined global functions or variables:
  read.delim read.xls
Consider adding
  importFrom("utils", "read.delim")
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 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/TargetScoreData.Rcheck/00check.log'
for details.



Installation output

TargetScoreData.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/TargetScoreData_1.27.0.tar.gz && rm -rf TargetScoreData.buildbin-libdir && mkdir TargetScoreData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TargetScoreData.buildbin-libdir TargetScoreData_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TargetScoreData_1.27.0.zip && rm TargetScoreData_1.27.0.tar.gz TargetScoreData_1.27.0.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
  3  206M    3 8360k    0     0  40.6M      0  0:00:05 --:--:--  0:00:05 40.4M
 45  206M   45 94.0M    0     0  79.1M      0  0:00:02  0:00:01  0:00:01 79.1M
 85  206M   85  176M    0     0  80.7M      0  0:00:02  0:00:02 --:--:-- 80.7M
100  206M  100  206M    0     0  80.5M      0  0:00:02  0:00:02 --:--:-- 80.5M

install for i386

* installing *source* package 'TargetScoreData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TargetScoreData'
    finding HTML links ... done
    TargetScoreData-package                 html  
REDIRECT:topic	 TargetScoreData-package -> TargetScoreData-package.html [ SUCCESS ]
REDIRECT:topic	 TargetScoreData -> TargetScoreData-package.html [ SUCCESS ]
    get_TargetScanHuman_PCT                 html  
REDIRECT:topic	 get_TargetScanHuman_PCT -> get_TargetScanHuman_PCT.html [ SUCCESS ]
    get_TargetScanHuman_contextScore        html  
REDIRECT:topic	 get_TargetScanHuman_contextScore -> get_TargetScanHuman_contextScore.html [ SUCCESS ]
    get_miRNA_family_info                   html  
REDIRECT:topic	 get_miRNA_family_info -> get_miRNA_family_info.html [ SUCCESS ]
    get_miRNA_transfection_data             html  
REDIRECT:topic	 get_miRNA_transfection_data -> get_miRNA_transfection_data.html [ SUCCESS ]
    get_precomputed_logFC                   html  
REDIRECT:topic	 get_precomputed_logFC -> get_precomputed_logFC.html [ SUCCESS ]
    get_precomputed_targetScores            html  
REDIRECT:topic	 get_precomputed_targetScores -> get_precomputed_targetScores.html [ SUCCESS ]
    get_validated_targets                   html  
REDIRECT:topic	 get_validated_targets -> get_validated_targets.html [ SUCCESS ]
** 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 'TargetScoreData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TargetScoreData' as TargetScoreData_1.27.0.zip
* DONE (TargetScoreData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'TargetScoreData' successfully unpacked and MD5 sums checked

Tests output


Example timings

TargetScoreData.Rcheck/examples_i386/TargetScoreData-Ex.timings

nameusersystemelapsed
TargetScoreData-package000

TargetScoreData.Rcheck/examples_x64/TargetScoreData-Ex.timings

nameusersystemelapsed
TargetScoreData-package000