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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 873/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GMRP 1.35.0  (landing page)
Yuan-De Tan
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/GMRP
git_branch: devel
git_last_commit: 261aa5d
git_last_commit_date: 2024-10-29 10:29:27 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for GMRP on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GMRP
Version: 1.35.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GMRP_1.35.0.tar.gz
StartedAt: 2024-12-24 07:18:44 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 07:20:11 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 87.0 seconds
RetCode: 0
Status:   OK  
CheckDir: GMRP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GMRP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GMRP_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GMRP.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GMRP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GMRP’ version ‘1.35.0’
* 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 ... OK
* 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 code 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 whether 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 ... NOTE
checkRd: (-1) cad.data.Rd:5: Lost braces
     5 | bold{GWAS} Meta-analyzed Data of Coronary Artery Disease
       |     ^
checkRd: (-1) chrp.Rd:15: Lost braces
    15 | character vector represented with code{chr##.#######} where chr## is chromosome number and \code{.#######} is SNP site (bp).
       |                                       ^
* 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/R/R-4.5.0-devel_2024-11-24/site-library/GMRP/doc/GMRP.R':
131:1: unexpected input
130: ###################################################
131: <<
     ^
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GMRP.Rcheck/00check.log’
for details.


Installation output

GMRP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GMRP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 in fun(libname, pkgname) :
  Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  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-package0.6320.0080.642
SNP358.data0.0020.0000.001
SNP368annot.data0.0010.0000.002
beta.data0.0010.0000.002
cad.data0.0110.0000.012
chrp0.0290.0040.034
fmerge0.0070.0000.008
lpd.data0.0280.0000.028
mktable0.0850.0000.085
path0.0140.0040.018
pathdiagram0.0480.0000.048
pathdiagram20.0690.0080.076
snpPositAnnot0.0540.0000.054
ucscannot0.0400.0040.044