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CHECK report for GMRP on merida1

This page was generated on 2019-04-16 12:10:43 -0400 (Tue, 16 Apr 2019).

Package 658/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GMRP 1.10.1
Yuan-De Tan
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GMRP
Branch: RELEASE_3_8
Last Commit: 7516bfb
Last Changed Date: 2018-11-26 09:36:26 -0400 (Mon, 26 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GMRP
Version: 1.10.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GMRP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GMRP_1.10.1.tar.gz
StartedAt: 2019-04-16 00:19:28 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:20:53 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 85.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GMRP.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GMRP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GMRP_1.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GMRP.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GMRP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GMRP’ version ‘1.10.1’
* 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 for sufficient/correct file permissions ... 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
See ‘/Users/biocbuild/bbs-3.8-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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GMRP.Rcheck/00check.log’
for details.



Installation output

GMRP.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GMRP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GMRP’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GMRP.Rnw’ 
** testing if installed package can be loaded
Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
* DONE (GMRP)

Tests output


Example timings

GMRP.Rcheck/GMRP-Ex.timings

nameusersystemelapsed
GMRP-package0.4110.0120.426
SNP358.data0.0030.0020.004
SNP368annot.data0.0020.0010.003
beta.data0.0010.0020.003
cad.data0.0160.0020.018
chrp0.0370.0030.041
fmerge0.0080.0010.009
lpd.data0.0360.0030.040
mktable0.1260.0160.147
path0.0200.0050.025
pathdiagram0.0600.0070.068
pathdiagram20.0950.0100.105
snpPositAnnot0.0630.0060.069
ucscannot0.0390.0080.048