| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:39 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 1295/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstats 4.9.1 (landing page) Meena Choi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: MSstats |
| Version: 4.9.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MSstats_4.9.1.tar.gz |
| StartedAt: 2023-05-30 13:09:42 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 13:11:53 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 130.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstats.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MSstats_4.9.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstats.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.9.1’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 7.979 0.096 8.075
dot-makeQCPlot 7.915 0.080 7.993
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/MSstats.Rcheck/00check.log’
for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘MSstats’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c common.cpp -o common.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c comparison_contrasts.cpp -o comparison_contrasts.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c linear_summary.cpp -o linear_summary.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c median_polish.cpp -o median_polish.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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;36m54ms[0m
[0;36m2ms[0m
All ok, 1 results (59ms)
>
> proc.time()
user system elapsed
3.691 0.157 3.831
MSstats.Rcheck/MSstats-Ex.timings
| name | user | system | elapsed | |
| DDARawData | 0.007 | 0.000 | 0.007 | |
| DDARawData.Skyline | 0.007 | 0.000 | 0.007 | |
| DIANNtoMSstatsFormat | 0 | 0 | 0 | |
| DIARawData | 0.004 | 0.000 | 0.004 | |
| DIAUmpiretoMSstatsFormat | 0.151 | 0.028 | 0.179 | |
| MSstatsGroupComparison | 0.425 | 0.008 | 0.435 | |
| MSstatsGroupComparisonOutput | 0.312 | 0.012 | 0.325 | |
| MSstatsGroupComparisonSingleProtein | 0.213 | 0.000 | 0.213 | |
| MSstatsHandleMissing | 0.117 | 0.000 | 0.109 | |
| MSstatsMergeFractions | 0.070 | 0.000 | 0.062 | |
| MSstatsNormalize | 0.068 | 0.004 | 0.064 | |
| MSstatsPrepareForDataProcess | 0.070 | 0.008 | 0.070 | |
| MSstatsPrepareForGroupComparison | 0.165 | 0.000 | 0.165 | |
| MSstatsPrepareForSummarization | 0.061 | 0.004 | 0.057 | |
| MSstatsSelectFeatures | 0.321 | 0.008 | 0.310 | |
| MSstatsSummarizationOutput | 0.360 | 0.024 | 0.370 | |
| MSstatsSummarize | 0.325 | 0.024 | 0.339 | |
| MSstatsSummarizeSingleLinear | 0.098 | 0.000 | 0.089 | |
| MSstatsSummarizeSingleTMP | 0.125 | 0.008 | 0.123 | |
| MaxQtoMSstatsFormat | 0.125 | 0.008 | 0.118 | |
| OpenMStoMSstatsFormat | 0.065 | 0.000 | 0.065 | |
| OpenSWATHtoMSstatsFormat | 0.080 | 0.003 | 0.083 | |
| PDtoMSstatsFormat | 0.064 | 0.003 | 0.067 | |
| ProgenesistoMSstatsFormat | 0.067 | 0.001 | 0.067 | |
| SRMRawData | 0.002 | 0.000 | 0.003 | |
| SkylinetoMSstatsFormat | 0.089 | 0.012 | 0.099 | |
| SpectronauttoMSstatsFormat | 0.064 | 0.000 | 0.063 | |
| checkRepeatedDesign | 0.163 | 0.004 | 0.167 | |
| dataProcess | 0.496 | 0.004 | 0.501 | |
| dataProcessPlots | 7.979 | 0.096 | 8.075 | |
| designSampleSize | 0.321 | 0.004 | 0.326 | |
| designSampleSizePlots | 0.342 | 0.012 | 0.354 | |
| dot-makeQCPlot | 7.915 | 0.080 | 7.993 | |
| getProcessed | 0.071 | 0.016 | 0.077 | |
| getSamplesInfo | 0.401 | 0.000 | 0.384 | |
| groupComparison | 0.282 | 0.000 | 0.282 | |
| groupComparisonPlots | 4.128 | 0.024 | 4.151 | |
| makePeptidesDictionary | 0.003 | 0.000 | 0.004 | |
| modelBasedQCPlots | 1.097 | 0.004 | 1.101 | |
| quantification | 0.224 | 0.000 | 0.224 | |