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This page was generated on 2024-04-17 11:37:08 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1604/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProteoMM 1.20.0  (landing page)
Yuliya V Karpievitch
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/ProteoMM
git_branch: RELEASE_3_18
git_last_commit: bdc1617
git_last_commit_date: 2023-10-24 11:08:54 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for ProteoMM on palomino4


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.

raw results


Summary

Package: ProteoMM
Version: 1.20.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ProteoMM.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ProteoMM_1.20.0.tar.gz
StartedAt: 2024-04-16 03:56:41 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 03:58:49 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 127.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ProteoMM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ProteoMM.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ProteoMM_1.20.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/ProteoMM.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ProteoMM/DESCRIPTION' ... OK
* this is package 'ProteoMM' version '1.20.0'
* 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 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 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 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       20.63   0.27   20.91
prot_level_multiMat_PresAbs  7.52   0.12    7.64
subset_proteins              7.03   0.17    7.22
get_presAbs_prots            6.50   0.11    6.61
peptideLevel_PresAbsDE       5.63   0.14    5.77
plot_volcano                 5.25   0.11    5.36
peptideLevel_DE              5.06   0.12    5.18
plot_volcano_wLab            4.87   0.14    5.01
* 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 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/ProteoMM.Rcheck/00check.log'
for details.



Installation output

ProteoMM.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ProteoMM
###
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##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'ProteoMM' ...
** 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
MBimpute4.440.114.55
convert_log2000
eig_norm14.040.064.11
eig_norm24.300.034.33
eigen_pi0.000.030.03
g.test000
get_presAbs_prots6.500.116.61
makeLMFormula000
make_intencities0.000.020.01
make_meta0.010.000.02
peptideLevel_DE5.060.125.18
peptideLevel_PresAbsDE5.630.145.77
plot_3_pep_trends_NOfile2.780.052.83
plot_volcano5.250.115.36
plot_volcano_wLab4.870.145.01
prot_level_multiMat_PresAbs7.520.127.64
prot_level_multi_part20.63 0.2720.91
subset_proteins7.030.177.22