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This page was generated on 2021-09-15 15:05:34 -0400 (Wed, 15 Sep 2021).

CHECK results for meshr on tokay2

To the developers/maintainers of the meshr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/meshr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1073/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
meshr 1.28.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2021-09-14 04:50:06 -0400 (Tue, 14 Sep 2021)
git_url: https://git.bioconductor.org/packages/meshr
git_branch: RELEASE_3_13
git_last_commit: f8913a9
git_last_commit_date: 2021-05-19 12:04:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: meshr
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings meshr_1.28.0.tar.gz
StartedAt: 2021-09-15 00:59:44 -0400 (Wed, 15 Sep 2021)
EndedAt: 2021-09-15 01:07:05 -0400 (Wed, 15 Sep 2021)
EllapsedTime: 440.7 seconds
RetCode: 0
Status:   OK  
CheckDir: meshr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings meshr_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/meshr.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.28.0'
* 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 'meshr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  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
** 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-3.13-bioc/meat/meshr.Rcheck/00check.log'
for details.



Installation output

meshr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/meshr_1.28.0.tar.gz && rm -rf meshr.buildbin-libdir && mkdir meshr.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=meshr.buildbin-libdir meshr_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL meshr_1.28.0.zip && rm meshr_1.28.0.tar.gz meshr_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  6 6341k    6  386k    0     0  1286k      0  0:00:04 --:--:--  0:00:04 1286k
 60 6341k   60 3832k    0     0  3012k      0  0:00:02  0:00:01  0:00:01 3012k
100 6341k  100 6341k    0     0  3383k      0  0:00:01  0:00:01 --:--:-- 3384k

install for i386

* installing *source* package 'meshr' ...
** using staged installation
** 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 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 'meshr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'meshr' as meshr_1.28.0.zip
* DONE (meshr)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'meshr' successfully unpacked and MD5 sums checked

Tests output


Example timings

meshr.Rcheck/examples_i386/meshr-Ex.timings

nameusersystemelapsed
PMCID3.720.414.12
category0.010.000.02
database000
geneid.cummeRbund0.000.020.01
meshHyperGTest000
meshr-package000
sig.geneid.cummeRbund0.020.000.02

meshr.Rcheck/examples_x64/meshr-Ex.timings

nameusersystemelapsed
PMCID4.280.154.44
category0.010.000.02
database000
geneid.cummeRbund0.000.020.01
meshHyperGTest000
meshr-package000
sig.geneid.cummeRbund0.020.000.02