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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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 1173/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metabCombiner 1.15.2  (landing page)
Hani Habra
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/metabCombiner
git_branch: devel
git_last_commit: d248824
git_last_commit_date: 2024-05-29 03:50:10 -0400 (Wed, 29 May 2024)
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 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for metabCombiner on kjohnson1

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: 1.15.2
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_1.15.2.tar.gz
StartedAt: 2024-06-11 00:20:56 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 00:23:26 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 149.2 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_1.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metabCombiner.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metabCombiner/DESCRIPTION’ ... OK
* this is package ‘metabCombiner’ version ‘1.15.2’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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-3.20-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/4.4-arm64/Resources/library’
* installing *source* package ‘metabCombiner’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c binByMZ.c -o binByMZ.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c duplicates.c -o duplicates.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c labelRows.c -o labelRows.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c metabCombiner_init.c -o metabCombiner_init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c resolveRows.c -o resolveRows.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c selectAnchors.c -o selectAnchors.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c write2file.c -o write2file.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 
 15.110   0.603  15.823 

Example timings

metabCombiner.Rcheck/metabCombiner-Ex.timings

nameusersystemelapsed
adductdata0.2820.0090.291
batchCombine0.0000.0010.000
calcScores1.5460.0551.601
calcScoresParam0.0000.0000.001
combineData0.2320.0050.238
combinedTable0.2300.0060.236
datasets0.5760.0090.594
evaluateParams3.2030.1023.330
featdata0.2250.0040.230
filtered0.1180.0040.122
fit_gam2.6700.0812.843
fit_loess1.9420.0251.971
fitgamParam0.0000.0000.001
fitloessParam0.0000.0010.000
getAnchors0.5750.0160.595
getCoefficients1.1670.0331.221
getData0.1120.0040.117
getExtra0.1150.0060.120
getModel0.7550.0230.818
getSamples0.4170.0120.440
getStats1.1580.0521.216
iddata0.2180.0050.224
labelRows1.9690.0782.052
labelRowsParam000
metabCombine0.0010.0000.000
metabCombiner0.4150.0120.427
metabData0.3440.0230.367
mzFit0.0010.0000.001
mzfitParam0.0000.0010.001
nonmatched0.2350.0050.247
opts.duplicate0.2230.0100.252
plot_fit0.7420.0200.762
rtdata0.2180.0050.223
selectAnchors1.1690.0291.206
selectAnchorsParam0.0010.0000.000
updateTables1.9540.1002.070
write2file1.8560.0531.916