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This page was generated on 2025-04-17 11:47 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1641/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProteoMM 1.26.0  (landing page)
Yuliya V Karpievitch
Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025)
git_url: https://git.bioconductor.org/packages/ProteoMM
git_branch: RELEASE_3_21
git_last_commit: 1dc9f34
git_last_commit_date: 2025-04-15 11:38:29 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    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 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ProteoMM on kunpeng2

To the developers/maintainers of the ProteoMM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ProteoMM.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: ProteoMM
Version: 1.26.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ProteoMM_1.26.0.tar.gz
StartedAt: 2025-04-17 10:17:10 -0000 (Thu, 17 Apr 2025)
EndedAt: 2025-04-17 10:19:43 -0000 (Thu, 17 Apr 2025)
EllapsedTime: 153.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ProteoMM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ProteoMM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ProteoMM_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ProteoMM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProteoMM/DESCRIPTION’ ... OK
* this is package ‘ProteoMM’ version ‘1.26.0’
* package encoding: UTF-8
* 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 ‘ProteoMM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
prot_level_multi_part       30.800  0.151  31.032
prot_level_multiMat_PresAbs 10.505  0.112  10.642
subset_proteins             10.437  0.044  10.507
get_presAbs_prots            8.352  0.012   8.384
peptideLevel_PresAbsDE       8.193  0.016   8.230
plot_volcano_wLab            6.939  0.012   6.967
peptideLevel_DE              6.351  0.036   6.403
MBimpute                     6.215  0.060   6.289
plot_volcano                 6.255  0.012   6.282
* checking for unstated dependencies in vignettes ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ProteoMM.Rcheck/00check.log’
for details.


Installation output

ProteoMM.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘ProteoMM’ ...
** this is package ‘ProteoMM’ version ‘1.26.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ProteoMM)

Tests output


Example timings

ProteoMM.Rcheck/ProteoMM-Ex.timings

nameusersystemelapsed
MBimpute6.2150.0606.289
convert_log20.0070.0000.007
eig_norm14.8270.0324.871
eig_norm24.8790.0204.910
eigen_pi0.0170.0040.021
g.test0.0040.0000.004
get_presAbs_prots8.3520.0128.384
makeLMFormula0.0010.0000.001
make_intencities0.0060.0000.006
make_meta0.0050.0000.006
peptideLevel_DE6.3510.0366.403
peptideLevel_PresAbsDE8.1930.0168.230
plot_3_pep_trends_NOfile4.3930.0004.404
plot_volcano6.2550.0126.282
plot_volcano_wLab6.9390.0126.967
prot_level_multiMat_PresAbs10.505 0.11210.642
prot_level_multi_part30.800 0.15131.032
subset_proteins10.437 0.04410.507