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CHECK report for GMRP on malbec2

This page was generated on 2019-10-16 12:15:06 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GMRP_1.12.0.tar.gz
StartedAt: 2019-10-16 02:03:45 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:05:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 90.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GMRP.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GMRP_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GMRP.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 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 ‘/home/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
* 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 ... 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/GMRP.Rcheck/00check.log’
for details.



Installation output

GMRP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GMRP
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GMRP’ ...
** using staged installation
** 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 from temporary location
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: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
** testing if installed package keeps a record of temporary installation path
* DONE (GMRP)

Tests output


Example timings

GMRP.Rcheck/GMRP-Ex.timings

nameusersystemelapsed
GMRP-package0.3840.0040.407
SNP358.data0.0010.0000.002
SNP368annot.data0.0000.0030.002
beta.data0.0010.0000.001
cad.data0.0170.0000.018
chrp0.0540.0000.054
fmerge0.010.000.01
lpd.data0.0440.0000.044
mktable0.1100.0040.114
path0.0140.0000.014
pathdiagram0.0560.0040.060
pathdiagram20.0850.0120.096
snpPositAnnot0.0480.0040.052
ucscannot0.040.000.04