Back to Multiple platform build/check report for BioC 3.12
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GMRP on malbec1

This page was generated on 2021-05-06 12:27:48 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GMRP package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 756/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GMRP 1.18.0  (landing page)
Yuan-De Tan
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GMRP
Branch: RELEASE_3_12
Last Commit: 3cf56a1
Last Changed Date: 2020-10-27 11:36:20 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GMRP
Version: 1.18.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GMRP_1.18.0.tar.gz
StartedAt: 2021-05-06 02:06:07 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:07:28 -0400 (Thu, 06 May 2021)
EllapsedTime: 80.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GMRP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GMRP_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/GMRP.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.18.0’
* 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-3.12-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-3.12-bioc/meat/GMRP.Rcheck/00check.log’
for details.



Installation output

GMRP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL GMRP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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-package0.4680.0080.492
SNP358.data0.0040.0000.002
SNP368annot.data0.0040.0000.003
beta.data0.0040.0000.001
cad.data0.0200.0000.019
chrp0.0520.0040.057
fmerge0.0080.0000.010
lpd.data0.0480.0000.046
mktable0.1280.0040.133
path0.0160.0040.018
pathdiagram0.0720.0000.070
pathdiagram20.1120.0000.115
snpPositAnnot0.0560.0040.061
ucscannot0.0400.0120.050