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This page was generated on 2023-01-31 11:09:53 -0500 (Tue, 31 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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

CHECK results for MSstats on lconway


To the developers/maintainers of the MSstats package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstats.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1283/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 4.6.3  (landing page)
Meena Choi
Snapshot Date: 2023-01-30 14:00:05 -0500 (Mon, 30 Jan 2023)
git_url: https://git.bioconductor.org/packages/MSstats
git_branch: RELEASE_3_16
git_last_commit: 09ea26d
git_last_commit_date: 2023-01-19 11:17:42 -0500 (Thu, 19 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstats
Version: 4.6.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.6.3.tar.gz
StartedAt: 2023-01-30 21:36:08 -0500 (Mon, 30 Jan 2023)
EndedAt: 2023-01-30 21:37:52 -0500 (Mon, 30 Jan 2023)
EllapsedTime: 104.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.6.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MSstats.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.6.3’
* 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 ‘MSstats’ can be installed ... OK
* 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 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 ... NOTE
.setCensoredByThreshold: no visible binding for global variable
  ‘any_censored’
Undefined global functions or variables:
  any_censored
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
dataProcessPlots 5.127  0.054   5.217
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/MSstats.Rcheck/00check.log’
for details.



Installation output

MSstats.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘MSstats’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c common.cpp -o common.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c comparison_contrasts.cpp -o comparison_contrasts.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c linear_summary.cpp -o linear_summary.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c median_polish.cpp -o median_polish.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-MSstats/00new/MSstats/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (MSstats)

Tests output

MSstats.Rcheck/tests/tinytest.Rout


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> if ( requireNamespace("tinytest", quietly=TRUE) ){
+   tinytest::test_package("MSstats")
+ }

Attaching package: 'MSstats'

The following object is masked from 'package:grDevices':

    savePlot


test_MSstatsdev.R.............    1 tests OK 55ms
2ms
All ok, 1 results (62ms)
> 
> proc.time()
   user  system elapsed 
  2.994   0.275   3.287 

Example timings

MSstats.Rcheck/MSstats-Ex.timings

nameusersystemelapsed
DDARawData0.0060.0020.008
DDARawData.Skyline0.0030.0010.004
DIANNtoMSstatsFormat0.0000.0000.001
DIARawData0.0010.0010.003
DIAUmpiretoMSstatsFormat0.1290.0220.151
MSstatsGroupComparison0.3670.0160.383
MSstatsGroupComparisonOutput0.2470.0080.256
MSstatsGroupComparisonSingleProtein0.1540.0050.160
MSstatsHandleMissing0.0550.0040.059
MSstatsMergeFractions0.0430.0040.047
MSstatsNormalize0.0410.0030.044
MSstatsPrepareForDataProcess0.0460.0020.048
MSstatsPrepareForGroupComparison0.1210.0040.126
MSstatsPrepareForSummarization0.0430.0020.046
MSstatsSelectFeatures0.2150.0120.229
MSstatsSummarizationOutput0.2290.0090.239
MSstatsSummarize0.2210.0090.232
MSstatsSummarizeSingleLinear0.0710.0030.073
MSstatsSummarizeSingleTMP0.0880.0050.093
MaxQtoMSstatsFormat0.1250.0100.136
OpenMStoMSstatsFormat0.0560.0020.059
OpenSWATHtoMSstatsFormat0.0490.0010.051
PDtoMSstatsFormat0.0540.0030.058
ProgenesistoMSstatsFormat0.0510.0030.053
SRMRawData0.0020.0000.002
SkylinetoMSstatsFormat0.0780.0050.083
SpectronauttoMSstatsFormat0.0360.0020.039
checkRepeatedDesign0.1640.0120.177
dataProcess0.3450.0090.355
dataProcessPlots5.1270.0545.217
designSampleSize0.2040.0100.215
designSampleSizePlots0.2480.0100.259
dot-makeQCPlot4.9230.0454.990
getProcessed0.0500.0030.054
getSamplesInfo0.2490.0060.258
groupComparison0.1940.0040.199
groupComparisonPlots2.6560.0352.702
makePeptidesDictionary0.0020.0000.003
modelBasedQCPlots0.7060.0120.722
quantification0.1440.0020.147