Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-27 11:35:40 -0400 (Wed, 27 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 855/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GMRP 1.28.0  (landing page)
Yuan-De Tan
Snapshot Date: 2023-09-26 14:00:14 -0400 (Tue, 26 Sep 2023)
git_url: https://git.bioconductor.org/packages/GMRP
git_branch: RELEASE_3_17
git_last_commit: c4c33b1
git_last_commit_date: 2023-04-25 11:02:39 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for GMRP on nebbiolo1


To the developers/maintainers of the GMRP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GMRP.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GMRP
Version: 1.28.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GMRP_1.28.0.tar.gz
StartedAt: 2023-09-26 21:49:11 -0400 (Tue, 26 Sep 2023)
EndedAt: 2023-09-26 21:50:33 -0400 (Tue, 26 Sep 2023)
EllapsedTime: 82.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GMRP.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GMRP_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GMRP.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GMRP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GMRP’ version ‘1.28.0’
* 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-3.17-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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ... NOTE
Warning: parse error in file '/home/biocbuild/bbs-3.17-bioc/R/site-library/GMRP/doc/GMRP.R':
131:1: unexpected input
130: ###################################################
131: <<
     ^
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GMRP.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GMRP.Rcheck/00check.log’
for details.



Installation output

GMRP.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GMRP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
** 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-package0.1790.0240.203
SNP358.data0.0010.0000.002
SNP368annot.data0.0020.0000.002
beta.data0.0010.0000.001
cad.data0.0080.0040.012
chrp0.0240.0040.028
fmerge0.0070.0000.007
lpd.data0.0210.0040.024
mktable0.0650.0080.073
path0.0100.0040.013
pathdiagram0.0360.0080.045
pathdiagram20.0670.0040.072
snpPositAnnot0.0450.0000.046
ucscannot0.0300.0040.034