Meena Choi
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MSstats |
| git_branch: RELEASE_3_17 |
| git_last_commit: 81aae3b |
| git_last_commit_date: 2023-07-28 09:34:56 -0400 (Fri, 28 Jul 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:33 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1314/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstats 4.8.7 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. - 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. |
| Package: MSstats |
| Version: 4.8.7 |
| 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_4.8.7.tar.gz |
| StartedAt: 2023-10-15 23:07:06 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 23:08:46 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 99.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstats.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_4.8.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSstats.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.8.7’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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’
DIANNtoMSstatsFormat: no visible binding for global variable
‘DetectionQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
‘LibPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
‘LibQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
‘GlobalPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
‘GlobalQValue’
Undefined global functions or variables:
DetectionQValue GlobalPGQValue GlobalQValue LibPGQValue LibQValue
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 5.499 0.036 5.487
dot-makeQCPlot 5.298 0.060 5.305
* 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-3.17-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 11.4.0-1ubuntu1~22.04) 11.4.0’ 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 -llapack -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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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;36m52ms[0m
[0;36m1ms[0m
All ok, 1 results (57ms)
>
> proc.time()
user system elapsed
2.683 0.229 2.894
MSstats.Rcheck/MSstats-Ex.timings
| name | user | system | elapsed | |
| DDARawData | 0.006 | 0.000 | 0.006 | |
| DDARawData.Skyline | 0.006 | 0.000 | 0.006 | |
| DIANNtoMSstatsFormat | 0 | 0 | 0 | |
| DIARawData | 0.003 | 0.000 | 0.003 | |
| DIAUmpiretoMSstatsFormat | 0.114 | 0.035 | 0.135 | |
| FragPipetoMSstatsFormat | 0.056 | 0.004 | 0.050 | |
| MSstatsGroupComparison | 0.277 | 0.004 | 0.281 | |
| MSstatsGroupComparisonOutput | 0.223 | 0.008 | 0.231 | |
| MSstatsGroupComparisonSingleProtein | 0.148 | 0.000 | 0.148 | |
| MSstatsHandleMissing | 0.136 | 0.000 | 0.088 | |
| MSstatsMergeFractions | 0.086 | 0.000 | 0.043 | |
| MSstatsNormalize | 0.086 | 0.000 | 0.045 | |
| MSstatsPrepareForDataProcess | 0.083 | 0.000 | 0.046 | |
| MSstatsPrepareForGroupComparison | 0.108 | 0.004 | 0.112 | |
| MSstatsPrepareForSummarization | 0.073 | 0.000 | 0.042 | |
| MSstatsSelectFeatures | 0.320 | 0.008 | 0.220 | |
| MSstatsSummarizationOutput | 0.292 | 0.008 | 0.230 | |
| MSstatsSummarize | 0.257 | 0.000 | 0.206 | |
| MSstatsSummarizeSingleLinear | 0.109 | 0.000 | 0.063 | |
| MSstatsSummarizeSingleTMP | 0.140 | 0.000 | 0.087 | |
| MaxQtoMSstatsFormat | 0.157 | 0.000 | 0.091 | |
| OpenMStoMSstatsFormat | 0.057 | 0.000 | 0.045 | |
| OpenSWATHtoMSstatsFormat | 0.056 | 0.004 | 0.050 | |
| PDtoMSstatsFormat | 0.057 | 0.000 | 0.048 | |
| ProgenesistoMSstatsFormat | 0.055 | 0.004 | 0.048 | |
| SRMRawData | 0.002 | 0.000 | 0.002 | |
| SkylinetoMSstatsFormat | 0.102 | 0.006 | 0.078 | |
| SpectronauttoMSstatsFormat | 0.058 | 0.001 | 0.044 | |
| checkRepeatedDesign | 0.109 | 0.004 | 0.114 | |
| dataProcess | 0.352 | 0.032 | 0.384 | |
| dataProcessPlots | 5.499 | 0.036 | 5.487 | |
| designSampleSize | 0.230 | 0.012 | 0.243 | |
| designSampleSizePlots | 0.251 | 0.004 | 0.255 | |
| dot-makeQCPlot | 5.298 | 0.060 | 5.305 | |
| getProcessed | 0.095 | 0.004 | 0.054 | |
| getSamplesInfo | 0.335 | 0.012 | 0.253 | |
| groupComparison | 0.185 | 0.000 | 0.185 | |
| groupComparisonPlots | 2.733 | 0.032 | 2.765 | |
| makePeptidesDictionary | 0.003 | 0.000 | 0.003 | |
| modelBasedQCPlots | 0.716 | 0.020 | 0.733 | |
| quantification | 0.133 | 0.010 | 0.142 | |