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This page was generated on 2022-05-20 12:05:37 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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 1259/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 4.4.1  (landing page)
Meena Choi
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/MSstats
git_branch: RELEASE_3_15
git_last_commit: e5dae55
git_last_commit_date: 2022-05-11 19:19:42 -0400 (Wed, 11 May 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstats
Version: 4.4.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSstats_4.4.1.tar.gz
StartedAt: 2022-05-19 20:30:34 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 20:32:05 -0400 (Thu, 19 May 2022)
EllapsedTime: 91.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstats.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSstats_4.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MSstats.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.4.1’
* 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
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/MSstats.Rcheck/00check.log’
for details.



Installation output

MSstats.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MSstats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘MSstats’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c common.cpp -o common.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c comparison_contrasts.cpp -o comparison_contrasts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c linear_summary.cpp -o linear_summary.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c median_polish.cpp -o median_polish.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 44ms
1ms
All ok, 1 results (48ms)
> 
> proc.time()
   user  system elapsed 
  2.821   0.187   2.990 

Example timings

MSstats.Rcheck/MSstats-Ex.timings

nameusersystemelapsed
DDARawData0.0030.0040.006
DDARawData.Skyline0.0010.0040.005
DIARawData0.0030.0000.003
DIAUmpiretoMSstatsFormat0.1650.0120.159
MSstatsGroupComparison0.6070.0440.652
MSstatsGroupComparisonOutput0.2320.0440.276
MSstatsGroupComparisonSingleProtein0.1690.0040.173
MSstatsHandleMissing0.1190.0040.068
MSstatsMergeFractions0.0820.0040.049
MSstatsNormalize0.0970.0000.053
MSstatsPrepareForDataProcess0.0920.0000.053
MSstatsPrepareForGroupComparison0.1280.0020.131
MSstatsPrepareForSummarization0.0890.0010.049
MSstatsSelectFeatures0.3450.0100.241
MSstatsSummarizationOutput0.3300.0090.270
MSstatsSummarize0.3070.0000.246
MSstatsSummarizeSingleLinear0.1230.0000.073
MSstatsSummarizeSingleTMP0.1580.0030.101
MaxQtoMSstatsFormat0.2070.0000.145
OpenMStoMSstatsFormat0.0650.0000.049
OpenSWATHtoMSstatsFormat0.0680.0000.054
PDtoMSstatsFormat0.0670.0120.066
ProgenesistoMSstatsFormat0.0610.0120.060
SRMRawData0.0000.0030.003
SkylinetoMSstatsFormat0.1060.0200.103
SpectronauttoMSstatsFormat0.0700.0040.059
checkRepeatedDesign0.1220.0040.126
dataProcess0.3600.0160.376
dataProcessPlots4.7050.0404.682
designSampleSize0.2720.0040.276
designSampleSizePlots0.2430.0120.255
dot-makeQCPlot4.4570.0324.446
getProcessed0.1130.0000.062
getSamplesInfo0.3730.0080.278
groupComparison0.2130.0120.225
groupComparisonPlots2.2000.0282.228
makePeptidesDictionary0.0050.0000.003
modelBasedQCPlots0.6200.0040.619
quantification0.1340.0040.138