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This page was generated on 2025-09-03 12:05 -0400 (Wed, 03 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4826
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4616
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1215/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metabCombiner 1.19.0  (landing page)
Hani Habra
Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 2025)
git_url: https://git.bioconductor.org/packages/metabCombiner
git_branch: devel
git_last_commit: 526b631
git_last_commit_date: 2025-04-15 12:12:26 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for metabCombiner on lconway

To the developers/maintainers of the metabCombiner package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metabCombiner.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: metabCombiner
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabCombiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabCombiner_1.19.0.tar.gz
StartedAt: 2025-09-02 21:53:28 -0400 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 21:56:06 -0400 (Tue, 02 Sep 2025)
EllapsedTime: 158.3 seconds
RetCode: 0
Status:   OK  
CheckDir: metabCombiner.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabCombiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabCombiner_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/metabCombiner.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metabCombiner/DESCRIPTION’ ... OK
* this is package ‘metabCombiner’ version ‘1.19.0’
* 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 ‘metabCombiner’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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) combineData.Rd:22: Lost braces
    22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}}
       |                          ^
checkRd: (-1) combineData.Rd:22: Lost braces
    22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}}
       |                                ^
checkRd: (-1) combineData.Rd:22: Lost braces
    22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}}
       |                                                          ^
checkRd: (-1) combineData.Rd:22: Lost braces
    22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}}
       |                                                                ^
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/metabCombiner.Rcheck/00check.log’
for details.


Installation output

metabCombiner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metabCombiner
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘metabCombiner’ ...
** this is package ‘metabCombiner’ version ‘1.19.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c binByMZ.c -o binByMZ.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c duplicates.c -o duplicates.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c labelRows.c -o labelRows.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c metabCombiner_init.c -o metabCombiner_init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c resolveRows.c -o resolveRows.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c selectAnchors.c -o selectAnchors.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c write2file.c -o write2file.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o metabCombiner.so binByMZ.o duplicates.o labelRows.o metabCombiner_init.o resolveRows.o selectAnchors.o write2file.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-metabCombiner/00new/metabCombiner/libs
** R
** data
** demo
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metabCombiner)

Tests output

metabCombiner.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(metabCombiner)
> 
> test_check("metabCombiner")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]
> 
> proc.time()
   user  system elapsed 
 15.528   0.664  16.320 

Example timings

metabCombiner.Rcheck/metabCombiner-Ex.timings

nameusersystemelapsed
adductdata0.2030.0070.212
batchCombine000
calcScores1.5080.0601.576
calcScoresParam000
combineData0.1810.0050.188
combinedTable0.1760.0040.181
datasets0.1800.0060.188
evaluateParams3.1850.1053.303
featdata0.1730.0040.178
filtered0.0790.0040.083
fit_gam2.4770.0452.538
fit_loess1.4040.0171.425
fitgamParam000
fitloessParam0.0010.0000.001
getAnchors0.4540.0130.469
getCoefficients1.2600.0321.297
getData0.0890.0030.093
getExtra0.1110.0100.122
getModel0.6170.0120.634
getSamples0.6220.0160.643
getStats0.9100.0290.947
iddata0.1660.0050.171
labelRows2.0410.0632.114
labelRowsParam000
metabCombine0.0000.0000.001
metabCombiner0.3000.0060.307
metabData0.2460.0180.265
mzFit0.0000.0010.000
mzfitParam0.0010.0000.000
nonmatched0.1710.0040.175
opts.duplicate0.1800.0090.190
plot_fit0.6010.0160.621
rtdata0.1670.0040.173
selectAnchors0.7060.0180.727
selectAnchorsParam0.0010.0000.000
updateTables1.9020.0651.982
write2file1.9740.0572.042