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CHECK report for GMRP on tokay2

This page was generated on 2019-10-16 12:41:47 -0400 (Wed, 16 Oct 2019).

Package 690/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GMRP 1.12.0
Yuan-De Tan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GMRP
Branch: RELEASE_3_9
Last Commit: 07f7c16
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 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: GMRP
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GMRP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GMRP_1.12.0.tar.gz
StartedAt: 2019-10-16 04:07:22 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:09:15 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 113.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GMRP.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:GMRP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GMRP_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GMRP.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 'GMRP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GMRP' version '1.12.0'
* 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 'GMRP' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GMRP.Rcheck/00install.out' for details.
* 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 installed files from 'inst/doc' ... 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GMRP.Rcheck/00check.log'
for details.



Installation output

GMRP.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/GMRP_1.12.0.tar.gz && rm -rf GMRP.buildbin-libdir && mkdir GMRP.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GMRP.buildbin-libdir GMRP_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GMRP_1.12.0.zip && rm GMRP_1.12.0.tar.gz GMRP_1.12.0.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  372k  100  372k    0     0  3920k      0 --:--:-- --:--:-- --:--:-- 4233k

install for i386

* installing *source* package 'GMRP' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
** help
*** installing help indices
  converting help for package 'GMRP'
    finding HTML links ... done
    GMRP-package                            html  
    SNP358.data                             html  
    SNP368annot.data                        html  
    beta.data                               html  
    cad.data                                html  
    chrp                                    html  
    fmerge                                  html  
    lpd.data                                html  
    mktable                                 html  
    path                                    html  
    pathdiagram                             html  
    pathdiagram2                            html  
    snpPositAnnot                           html  
    ucscannot                               html  
** building package indices
** installing vignettes
   'GMRP.Rnw' 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
** testing if installed package can be loaded from final location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GMRP' ...
** testing if installed package can be loaded
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
* MD5 sums
packaged installation of 'GMRP' as GMRP_1.12.0.zip
* DONE (GMRP)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GMRP' successfully unpacked and MD5 sums checked

Tests output


Example timings

GMRP.Rcheck/examples_i386/GMRP-Ex.timings

nameusersystemelapsed
GMRP-package0.270.030.29
SNP358.data000
SNP368annot.data0.000.010.02
beta.data000
cad.data0.030.000.03
chrp0.060.020.08
fmerge0.020.000.01
lpd.data0.040.010.07
mktable0.380.000.37
path0.010.000.01
pathdiagram0.080.000.08
pathdiagram20.110.030.14
snpPositAnnot0.060.020.08
ucscannot0.050.000.05

GMRP.Rcheck/examples_x64/GMRP-Ex.timings

nameusersystemelapsed
GMRP-package0.270.010.28
SNP358.data000
SNP368annot.data0.000.020.02
beta.data0.020.000.02
cad.data0.010.000.01
chrp0.070.010.08
fmerge0.010.000.01
lpd.data0.050.020.07
mktable0.450.010.47
path0.020.020.03
pathdiagram0.090.000.09
pathdiagram20.140.000.14
snpPositAnnot0.070.020.08
ucscannot0.030.010.05