Meena Choi
| Snapshot Date: 2023-10-15 14:00:07 -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 Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the MSstats package: - 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.8.7.tar.gz |
| StartedAt: 2023-10-18 09:59:31 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 10:02:49 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 197.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstats.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.8.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstats.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 6.972 0.101 10.979
dot-makeQCPlot 6.813 0.092 10.636
groupComparisonPlots 3.763 0.067 5.963
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstats.Rcheck/00check.log’
for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘MSstats’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c common.cpp -o common.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c comparison_contrasts.cpp -o comparison_contrasts.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c linear_summary.cpp -o linear_summary.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c median_polish.cpp -o median_polish.o clang++ -arch arm64 -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/opt/R/arm64/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/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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;36m78ms[0m
[0;36m2ms[0m
All ok, 1 results (86ms)
>
> proc.time()
user system elapsed
3.357 0.267 5.637
MSstats.Rcheck/MSstats-Ex.timings
| name | user | system | elapsed | |
| DDARawData | 0.006 | 0.002 | 0.012 | |
| DDARawData.Skyline | 0.005 | 0.001 | 0.010 | |
| DIANNtoMSstatsFormat | 0.000 | 0.000 | 0.001 | |
| DIARawData | 0.002 | 0.001 | 0.005 | |
| DIAUmpiretoMSstatsFormat | 0.152 | 0.025 | 0.286 | |
| FragPipetoMSstatsFormat | 0.052 | 0.009 | 0.096 | |
| MSstatsGroupComparison | 0.395 | 0.019 | 0.641 | |
| MSstatsGroupComparisonOutput | 0.310 | 0.009 | 0.492 | |
| MSstatsGroupComparisonSingleProtein | 0.193 | 0.004 | 0.303 | |
| MSstatsHandleMissing | 0.071 | 0.004 | 0.111 | |
| MSstatsMergeFractions | 0.054 | 0.003 | 0.086 | |
| MSstatsNormalize | 0.053 | 0.003 | 0.097 | |
| MSstatsPrepareForDataProcess | 0.058 | 0.004 | 0.105 | |
| MSstatsPrepareForGroupComparison | 0.133 | 0.003 | 0.220 | |
| MSstatsPrepareForSummarization | 0.045 | 0.002 | 0.074 | |
| MSstatsSelectFeatures | 0.263 | 0.008 | 0.418 | |
| MSstatsSummarizationOutput | 0.285 | 0.007 | 0.452 | |
| MSstatsSummarize | 0.280 | 0.007 | 0.442 | |
| MSstatsSummarizeSingleLinear | 0.081 | 0.002 | 0.124 | |
| MSstatsSummarizeSingleTMP | 0.105 | 0.003 | 0.157 | |
| MaxQtoMSstatsFormat | 0.171 | 0.015 | 0.305 | |
| OpenMStoMSstatsFormat | 0.062 | 0.003 | 0.101 | |
| OpenSWATHtoMSstatsFormat | 0.063 | 0.004 | 0.109 | |
| PDtoMSstatsFormat | 0.059 | 0.005 | 0.101 | |
| ProgenesistoMSstatsFormat | 0.063 | 0.005 | 0.113 | |
| SRMRawData | 0.002 | 0.001 | 0.006 | |
| SkylinetoMSstatsFormat | 0.098 | 0.010 | 0.171 | |
| SpectronauttoMSstatsFormat | 0.055 | 0.003 | 0.094 | |
| checkRepeatedDesign | 0.177 | 0.007 | 0.279 | |
| dataProcess | 0.440 | 0.012 | 0.697 | |
| dataProcessPlots | 6.972 | 0.101 | 10.979 | |
| designSampleSize | 0.318 | 0.016 | 0.512 | |
| designSampleSizePlots | 0.304 | 0.015 | 0.496 | |
| dot-makeQCPlot | 6.813 | 0.092 | 10.636 | |
| getProcessed | 0.064 | 0.003 | 0.105 | |
| getSamplesInfo | 0.337 | 0.006 | 0.527 | |
| groupComparison | 0.254 | 0.004 | 0.415 | |
| groupComparisonPlots | 3.763 | 0.067 | 5.963 | |
| makePeptidesDictionary | 0.003 | 0.001 | 0.004 | |
| modelBasedQCPlots | 1.025 | 0.021 | 1.743 | |
| quantification | 0.198 | 0.006 | 0.356 | |