Meena Choi
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MSstats |
| git_branch: RELEASE_3_13 |
| git_last_commit: afa9e58 |
| git_last_commit_date: 2021-05-31 23:11:01 -0400 (Mon, 31 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1208/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstats 4.0.1 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MSstats |
| Version: 4.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstats_4.0.1.tar.gz |
| StartedAt: 2021-10-14 21:28:24 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:30:38 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 133.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstats.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstats_4.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MSstats.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘4.0.1’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
dot-makeQCPlot 7.061 0.027 7.097
dataProcessPlots 6.616 0.046 6.670
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/MSstats.Rcheck/00check.log’
for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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 installing to /Library/Frameworks/R.framework/Versions/4.1/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)
MSstats.Rcheck/tests/tinytest.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 [0;32mOK[0m [0;36m58ms[0m
[0;36m2ms[0m
All ok, 1 results (63ms)
>
> proc.time()
user system elapsed
3.944 0.251 4.180
MSstats.Rcheck/MSstats-Ex.timings
| name | user | system | elapsed | |
| DDARawData | 0.011 | 0.002 | 0.013 | |
| DDARawData.Skyline | 0.095 | 0.002 | 0.097 | |
| DIARawData | 0.006 | 0.001 | 0.006 | |
| DIAUmpiretoMSstatsFormat | 0.430 | 0.015 | 0.447 | |
| MSstatsGroupComparison | 0.596 | 0.065 | 0.670 | |
| MSstatsGroupComparisonOutput | 0.437 | 0.023 | 0.461 | |
| MSstatsGroupComparisonSingleProtein | 0.291 | 0.006 | 0.297 | |
| MSstatsHandleMissing | 0.100 | 0.004 | 0.105 | |
| MSstatsMergeFractions | 0.080 | 0.005 | 0.086 | |
| MSstatsNormalize | 0.089 | 0.005 | 0.095 | |
| MSstatsPrepareForDataProcess | 0.090 | 0.005 | 0.095 | |
| MSstatsPrepareForGroupComparison | 0.191 | 0.005 | 0.196 | |
| MSstatsPrepareForSummarization | 0.080 | 0.006 | 0.085 | |
| MSstatsSelectFeatures | 0.338 | 0.019 | 0.357 | |
| MSstatsSummarizationOutput | 0.315 | 0.010 | 0.326 | |
| MSstatsSummarize | 0.403 | 0.008 | 0.412 | |
| MSstatsSummarizeSingleLinear | 0.128 | 0.004 | 0.132 | |
| MSstatsSummarizeSingleTMP | 0.131 | 0.003 | 0.134 | |
| MaxQtoMSstatsFormat | 0.205 | 0.007 | 0.213 | |
| OpenMStoMSstatsFormat | 0.085 | 0.002 | 0.086 | |
| OpenSWATHtoMSstatsFormat | 0.107 | 0.005 | 0.113 | |
| PDtoMSstatsFormat | 0.063 | 0.002 | 0.065 | |
| ProgenesistoMSstatsFormat | 0.086 | 0.002 | 0.089 | |
| SRMRawData | 0.004 | 0.001 | 0.005 | |
| SkylinetoMSstatsFormat | 0.127 | 0.007 | 0.133 | |
| SpectronauttoMSstatsFormat | 0.076 | 0.003 | 0.078 | |
| checkRepeatedDesign | 0.211 | 0.002 | 0.213 | |
| dataProcess | 0.518 | 0.011 | 0.529 | |
| dataProcessPlots | 6.616 | 0.046 | 6.670 | |
| designSampleSize | 0.423 | 0.013 | 0.437 | |
| designSampleSizePlots | 0.404 | 0.011 | 0.416 | |
| dot-makeQCPlot | 7.061 | 0.027 | 7.097 | |
| getProcessed | 0.073 | 0.005 | 0.077 | |
| getSamplesInfo | 0.417 | 0.009 | 0.427 | |
| groupComparison | 0.545 | 0.005 | 0.550 | |
| groupComparisonPlots | 3.155 | 0.019 | 3.180 | |
| makePeptidesDictionary | 0.005 | 0.000 | 0.005 | |
| modelBasedQCPlots | 0.827 | 0.010 | 0.837 | |
| quantification | 0.189 | 0.003 | 0.192 | |