| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
To the developers/maintainers of the MSstats package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1303/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstats 4.7.2 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: MSstats |
| Version: 4.7.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MSstats_4.7.2.tar.gz |
| StartedAt: 2023-04-12 07:43:29 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 07:45:39 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 130.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstats.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MSstats_4.7.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSstats.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.7.2’
* 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 ‘MSstats’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 5.6Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘statmod’
All declared Imports should be used.
* 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 6.559 0.072 6.589
dot-makeQCPlot 6.372 0.112 6.452
* 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 ...
‘MSstats.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MSstats.Rcheck/00check.log’
for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘MSstats’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-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-3.17-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-3.17-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-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)
MSstats.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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 [0;32mOK[0m [0;36m48ms[0m
[0;36m1ms[0m
All ok, 1 results (52ms)
>
> proc.time()
user system elapsed
3.725 0.235 3.945
MSstats.Rcheck/MSstats-Ex.timings
| name | user | system | elapsed | |
| DDARawData | 0.006 | 0.000 | 0.006 | |
| DDARawData.Skyline | 0.001 | 0.004 | 0.005 | |
| DIANNtoMSstatsFormat | 0 | 0 | 0 | |
| DIARawData | 0.003 | 0.000 | 0.003 | |
| DIAUmpiretoMSstatsFormat | 0.122 | 0.031 | 0.137 | |
| MSstatsGroupComparison | 0.320 | 0.005 | 0.324 | |
| MSstatsGroupComparisonOutput | 0.241 | 0.004 | 0.246 | |
| MSstatsGroupComparisonSingleProtein | 0.154 | 0.000 | 0.154 | |
| MSstatsHandleMissing | 0.149 | 0.000 | 0.100 | |
| MSstatsMergeFractions | 0.104 | 0.000 | 0.054 | |
| MSstatsNormalize | 0.107 | 0.004 | 0.058 | |
| MSstatsPrepareForDataProcess | 0.112 | 0.000 | 0.060 | |
| MSstatsPrepareForGroupComparison | 0.117 | 0.000 | 0.117 | |
| MSstatsPrepareForSummarization | 0.084 | 0.000 | 0.046 | |
| MSstatsSelectFeatures | 0.380 | 0.008 | 0.259 | |
| MSstatsSummarizationOutput | 0.344 | 0.000 | 0.263 | |
| MSstatsSummarize | 0.299 | 0.000 | 0.235 | |
| MSstatsSummarizeSingleLinear | 0.136 | 0.000 | 0.078 | |
| MSstatsSummarizeSingleTMP | 0.164 | 0.000 | 0.100 | |
| MaxQtoMSstatsFormat | 0.186 | 0.004 | 0.110 | |
| OpenMStoMSstatsFormat | 0.058 | 0.004 | 0.047 | |
| OpenSWATHtoMSstatsFormat | 0.066 | 0.000 | 0.055 | |
| PDtoMSstatsFormat | 0.066 | 0.000 | 0.055 | |
| ProgenesistoMSstatsFormat | 0.062 | 0.000 | 0.051 | |
| SRMRawData | 0.002 | 0.000 | 0.002 | |
| SkylinetoMSstatsFormat | 0.118 | 0.019 | 0.115 | |
| SpectronauttoMSstatsFormat | 0.052 | 0.011 | 0.051 | |
| checkRepeatedDesign | 0.126 | 0.001 | 0.127 | |
| dataProcess | 0.444 | 0.004 | 0.448 | |
| dataProcessPlots | 6.559 | 0.072 | 6.589 | |
| designSampleSize | 0.257 | 0.000 | 0.256 | |
| designSampleSizePlots | 0.283 | 0.000 | 0.283 | |
| dot-makeQCPlot | 6.372 | 0.112 | 6.452 | |
| getProcessed | 0.103 | 0.000 | 0.055 | |
| getSamplesInfo | 0.348 | 0.008 | 0.262 | |
| groupComparison | 0.206 | 0.004 | 0.210 | |
| groupComparisonPlots | 3.852 | 0.016 | 3.868 | |
| makePeptidesDictionary | 0.003 | 0.000 | 0.003 | |
| modelBasedQCPlots | 0.792 | 0.000 | 0.786 | |
| quantification | 0.156 | 0.004 | 0.160 | |