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CHECK report for meshes on tokay2

This page was generated on 2018-10-04 10:55:11 -0400 (Thu, 04 Oct 2018).

Package 862/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
meshes 1.6.1
Guangchuang Yu
Snapshot Date: 2018-10-03 16:45:15 -0400 (Wed, 03 Oct 2018)
URL: https://git.bioconductor.org/packages/meshes
Branch: RELEASE_3_7
Last Commit: b36374f
Last Changed Date: 2018-05-25 02:08:03 -0400 (Fri, 25 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: meshes
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshes.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings meshes_1.6.1.tar.gz
StartedAt: 2018-10-04 03:06:06 -0400 (Thu, 04 Oct 2018)
EndedAt: 2018-10-04 03:09:40 -0400 (Thu, 04 Oct 2018)
EllapsedTime: 214.5 seconds
RetCode: 0
Status:  OK  
CheckDir: meshes.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshes.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings meshes_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/meshes.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'meshes/DESCRIPTION' ... OK
* this is package 'meshes' version '1.6.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'meshes' 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
Examples with CPU or elapsed time > 5s
         user system elapsed
meshdata 7.93   1.05   26.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
meshdata  9.4   0.89   10.29
* 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

meshes.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/meshes_1.6.1.tar.gz && rm -rf meshes.buildbin-libdir && mkdir meshes.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=meshes.buildbin-libdir meshes_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL meshes_1.6.1.zip && rm meshes_1.6.1.tar.gz meshes_1.6.1.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  882k  100  882k    0     0  12.1M      0 --:--:-- --:--:-- --:--:-- 13.2M

install for i386

* installing *source* package 'meshes' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'meshes'
    finding HTML links ... done
    enrichMeSH                              html  
    geneSim                                 html  
    gseMeSH                                 html  
    meshSim                                 html  
    mesh_term_table                         html  
    meshdata                                html  
    reexports                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'meshes' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'meshes' as meshes_1.6.1.zip
* DONE (meshes)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'meshes' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

meshes.Rcheck/examples_i386/meshes-Ex.timings

nameusersystemelapsed
enrichMeSH0.010.000.01
geneSim3.300.123.44
gseMeSH000
meshSim1.030.021.05
meshdata 7.93 1.0526.68

meshes.Rcheck/examples_x64/meshes-Ex.timings

nameusersystemelapsed
enrichMeSH000
geneSim3.780.083.86
gseMeSH000
meshSim1.110.031.14
meshdata 9.40 0.8910.29