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CHECK report for GenomicScores on tokay2

This page was generated on 2019-10-16 12:38:17 -0400 (Wed, 16 Oct 2019).

Package 660/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicScores 1.8.1
Robert Castelo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GenomicScores
Branch: RELEASE_3_9
Last Commit: f6303d9
Last Changed Date: 2019-06-22 08:06:47 -0400 (Sat, 22 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicScores
Version: 1.8.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicScores.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicScores_1.8.1.tar.gz
StartedAt: 2019-10-16 03:59:02 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:05:25 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 383.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicScores.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicScores.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicScores_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicScores.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicScores/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicScores' version '1.8.1'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/gscores-template/inst/extdata/.gitkeep
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GenomicScores' 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 ... WARNING
Missing link or links in documentation object 'GScores-class.Rd':
  'phastCons100way.UCSC.hg19'

Missing link or links in documentation object 'gscores.Rd':
  'phastCons100way.UCSC.hg19' 'MafDb.1Kgenomes.phase1.hs37d5'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
gscores       18.64   3.52   25.36
GScores-class  8.94   0.57   26.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
gscores       19.13   3.31   22.61
GScores-class  9.41   0.58   10.57
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicScores.Rcheck/00check.log'
for details.



Installation output

GenomicScores.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GenomicScores_1.8.1.tar.gz && rm -rf GenomicScores.buildbin-libdir && mkdir GenomicScores.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicScores.buildbin-libdir GenomicScores_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GenomicScores_1.8.1.zip && rm GenomicScores_1.8.1.tar.gz GenomicScores_1.8.1.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 1742k  100 1742k    0     0  21.3M      0 --:--:-- --:--:-- --:--:-- 23.3M

install for i386

* installing *source* package 'GenomicScores' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'score' with signature '"MafDb"': no definition for class "MafDb"
** help
*** installing help indices
  converting help for package 'GenomicScores'
    finding HTML links ... done
    GScores-class                           html  
    finding level-2 HTML links ... done

    GenomicScores-defunct                   html  
    GenomicScores-deprecated                html  
    gscores                                 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 'GenomicScores' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicScores' as GenomicScores_1.8.1.zip
* DONE (GenomicScores)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GenomicScores' successfully unpacked and MD5 sums checked

Tests output


Example timings

GenomicScores.Rcheck/examples_i386/GenomicScores-Ex.timings

nameusersystemelapsed
GScores-class 8.94 0.5726.53
gscores18.64 3.5225.36

GenomicScores.Rcheck/examples_x64/GenomicScores-Ex.timings

nameusersystemelapsed
GScores-class 9.41 0.5810.57
gscores19.13 3.3122.61