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CHECK report for meshr on tokay1

This page was generated on 2019-04-13 11:23:50 -0400 (Sat, 13 Apr 2019).

Package 912/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
meshr 1.18.0
Koki Tsuyuzaki
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/meshr
Branch: RELEASE_3_8
Last Commit: b3bb9d7
Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: meshr
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings meshr_1.18.0.tar.gz
StartedAt: 2019-04-13 03:38:31 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:46:27 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 475.8 seconds
RetCode: 0
Status:  OK  
CheckDir: meshr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings meshr_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/meshr.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'meshr/DESCRIPTION' ... OK
* this is package 'meshr' version '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'meshr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: 'Category:::.doHyperGInternal'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convert_PMID_PMCID: no visible binding for global variable 'PMCID'
save.pdf,MeSHHyperGResult : <anonymous>: no visible binding for global
  variable 'PMCID'
Undefined global functions or variables:
  PMCID
* 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 or elapsed time > 5s
      user system elapsed
PMCID 5.42   0.63     6.1
** 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/meshr.Rcheck/00check.log'
for details.



Installation output

meshr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/meshr_1.18.0.tar.gz && rm -rf meshr.buildbin-libdir && mkdir meshr.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=meshr.buildbin-libdir meshr_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL meshr_1.18.0.zip && rm meshr_1.18.0.tar.gz meshr_1.18.0.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 6342k  100 6342k    0     0  66.9M      0 --:--:-- --:--:-- --:--:-- 69.5M

install for i386

* installing *source* package 'meshr' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'meshr'
    finding HTML links ... done
    MeSHHyperGParams-class                  html  
    MeSHHyperGResult-class                  html  
    PMCID                                   html  
    category                                html  
    database                                html  
    geneid.cummeRbund                       html  
    meshHyperGTest                          html  
    meshr-package                           html  
    sig.geneid.cummeRbund                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'meshr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'meshr' as meshr_1.18.0.zip
* DONE (meshr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'meshr' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

meshr.Rcheck/examples_i386/meshr-Ex.timings

nameusersystemelapsed
PMCID5.420.636.10
category000
database000
geneid.cummeRbund0.000.000.02
meshHyperGTest000
meshr-package000
sig.geneid.cummeRbund0.000.000.02

meshr.Rcheck/examples_x64/meshr-Ex.timings

nameusersystemelapsed
PMCID3.770.163.92
category000
database000
geneid.cummeRbund000
meshHyperGTest000
meshr-package000
sig.geneid.cummeRbund0.000.020.01