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This page was generated on 2024-05-16 11:37:12 -0400 (Thu, 16 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1206/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metabCombiner 1.14.0  (landing page)
Hani Habra
Snapshot Date: 2024-05-15 14:00:14 -0400 (Wed, 15 May 2024)
git_url: https://git.bioconductor.org/packages/metabCombiner
git_branch: RELEASE_3_19
git_last_commit: 734d615
git_last_commit_date: 2024-04-30 11:28:28 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64see weekly results here

CHECK results for metabCombiner on palomino3


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: 1.14.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabCombiner.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings metabCombiner_1.14.0.tar.gz
StartedAt: 2024-05-16 03:43:25 -0400 (Thu, 16 May 2024)
EndedAt: 2024-05-16 03:46:06 -0400 (Thu, 16 May 2024)
EllapsedTime: 161.3 seconds
RetCode: 0
Status:   OK  
CheckDir: metabCombiner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabCombiner.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings metabCombiner_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/metabCombiner.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'metabCombiner/DESCRIPTION' ... OK
* this is package 'metabCombiner' version '1.14.0'
* 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 'metabCombiner' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/metabCombiner/libs/x64/metabCombiner.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/metabCombiner.Rcheck/00check.log'
for details.


Installation output

metabCombiner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL metabCombiner
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'metabCombiner' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c binByMZ.c -o binByMZ.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c duplicates.c -o duplicates.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c labelRows.c -o labelRows.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c metabCombiner_init.c -o metabCombiner_init.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c resolveRows.c -o resolveRows.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c selectAnchors.c -o selectAnchors.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c write2file.c -o write2file.o
gcc -shared -s -static-libgcc -o metabCombiner.dll tmp.def binByMZ.o duplicates.o labelRows.o metabCombiner_init.o resolveRows.o selectAnchors.o write2file.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-metabCombiner/00new/metabCombiner/libs/x64
** 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
** 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 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  14.62    0.96   15.56 

Example timings

metabCombiner.Rcheck/metabCombiner-Ex.timings

nameusersystemelapsed
adductdata0.180.020.21
batchCombine000
calcScores1.190.031.24
calcScoresParam000
combineData0.170.000.18
combinedTable0.160.000.15
datasets0.150.010.17
evaluateParams3.470.143.61
featdata0.160.000.16
filtered0.110.000.11
fit_gam2.430.102.53
fit_loess1.430.041.47
fitgamParam000
fitloessParam000
getAnchors0.450.020.47
getCoefficients1.240.051.28
getData0.080.000.08
getExtra0.090.000.10
getModel0.920.010.94
getSamples0.300.060.36
getStats1.020.021.03
iddata0.140.030.17
labelRows1.670.081.75
labelRowsParam000
metabCombine000
metabCombiner0.450.030.49
metabData0.360.000.36
nonmatched0.220.020.24
opts.duplicate0.250.010.26
plot_fit0.670.030.70
rtdata0.220.020.24
selectAnchors0.660.030.69
selectAnchorsParam000
updateTables1.890.081.96
write2file2.010.172.19