Meena Choi
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/MSstats |
| git_branch: RELEASE_3_18 |
| git_last_commit: c4264fc |
| git_last_commit_date: 2024-02-28 16:17:00 -0400 (Wed, 28 Feb 2024) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:14 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1342/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstats 4.10.1 (landing page) Meena Choi
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | 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: 4.10.1 |
| 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_4.10.1.tar.gz |
| StartedAt: 2024-04-17 20:40:53 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 20:44:09 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 195.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstats.Rcheck |
| Warnings: 2 |
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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_4.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MSstats.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.10.1’
* 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 ... WARNING
Found the following significant warnings:
linear_summary.cpp:65:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
linear_summary.cpp:88:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MSstats.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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.
Unexported object imported by a ':::' call: ‘MSstatsConvert:::.standardizeColnames’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotHeatmap : <anonymous>: no visible global function definition for
‘col2rgb’
.plotProfile: no visible binding for global variable ‘newABUNDANCE’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
.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’
MSstatsPrepareForSummarization: no visible binding for global variable
‘ref’
MSstatsPrepareForSummarization: no visible binding for global variable
‘LABEL’
MSstatsPrepareForSummarization: no visible binding for global variable
‘RUN’
SDRFtoAnnotation: no visible binding for global variable
‘..extract_cols’
extractSDRF: no visible binding for global variable ‘..extract_cols’
Undefined global functions or variables:
..extract_cols DetectionQValue GlobalPGQValue GlobalQValue LABEL
LibPGQValue LibQValue RUN any_censored col2rgb newABUNDANCE ref zip
Consider adding
importFrom("grDevices", "col2rgb")
importFrom("utils", "zip")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘example_SDRF’
Undocumented data sets:
‘example_SDRF’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 5.728 0.087 5.874
dot-makeQCPlot 5.101 0.047 5.210
* 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: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MSstats.Rcheck/00check.log’
for details.
MSstats.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstats
###
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* 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 15.0.0 (clang-1500.0.40.1)’
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
linear_summary.cpp:65:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if ((find_ref.length() != 0) & !(find_ref[0] == -1)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
linear_summary.cpp:65:9: note: cast one or both operands to int to silence this warning
linear_summary.cpp:88:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if ((find_run_feature.length() != 0) & !(find_run_feature[0] == -1)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
linear_summary.cpp:88:9: note: cast one or both operands to int to silence this warning
2 warnings generated.
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 -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
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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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;36m60ms[0m
[0;36m2ms[0m
All ok, 1 results (66ms)
>
> proc.time()
user system elapsed
3.518 0.250 3.798
MSstats.Rcheck/MSstats-Ex.timings
| name | user | system | elapsed | |
| DDARawData | 0.007 | 0.001 | 0.009 | |
| DDARawData.Skyline | 0.006 | 0.002 | 0.007 | |
| DIANNtoMSstatsFormat | 0 | 0 | 0 | |
| DIARawData | 0.002 | 0.001 | 0.003 | |
| DIAUmpiretoMSstatsFormat | 0.152 | 0.016 | 0.170 | |
| FragPipetoMSstatsFormat | 0.042 | 0.004 | 0.047 | |
| MSstatsGroupComparison | 0.287 | 0.013 | 0.299 | |
| MSstatsGroupComparisonOutput | 0.254 | 0.007 | 0.261 | |
| MSstatsGroupComparisonSingleProtein | 0.161 | 0.004 | 0.166 | |
| MSstatsHandleMissing | 0.051 | 0.001 | 0.053 | |
| MSstatsMergeFractions | 0.049 | 0.002 | 0.051 | |
| MSstatsNormalize | 0.056 | 0.003 | 0.058 | |
| MSstatsPrepareForDataProcess | 0.043 | 0.002 | 0.044 | |
| MSstatsPrepareForGroupComparison | 0.116 | 0.004 | 0.120 | |
| MSstatsPrepareForSummarization | 0.055 | 0.003 | 0.057 | |
| MSstatsSelectFeatures | 0.281 | 0.013 | 0.294 | |
| MSstatsSummarizationOutput | 0.236 | 0.008 | 0.244 | |
| MSstatsSummarize | 0.241 | 0.010 | 0.251 | |
| MSstatsSummarizeSingleLinear | 0.067 | 0.002 | 0.069 | |
| MSstatsSummarizeSingleTMP | 0.096 | 0.006 | 0.102 | |
| MaxQtoMSstatsFormat | 0.144 | 0.012 | 0.159 | |
| OpenMStoMSstatsFormat | 0.056 | 0.003 | 0.059 | |
| OpenSWATHtoMSstatsFormat | 0.048 | 0.003 | 0.051 | |
| PDtoMSstatsFormat | 0.053 | 0.003 | 0.057 | |
| ProgenesistoMSstatsFormat | 0.054 | 0.003 | 0.058 | |
| SDRFtoAnnotation | 0.013 | 0.002 | 0.014 | |
| SRMRawData | 0.002 | 0.000 | 0.003 | |
| SkylinetoMSstatsFormat | 0.084 | 0.008 | 0.093 | |
| SpectronauttoMSstatsFormat | 0.045 | 0.002 | 0.048 | |
| checkRepeatedDesign | 0.119 | 0.003 | 0.123 | |
| dataProcess | 0.352 | 0.013 | 0.365 | |
| dataProcessPlots | 5.728 | 0.087 | 5.874 | |
| designSampleSize | 0.226 | 0.013 | 0.239 | |
| designSampleSizePlots | 0.255 | 0.012 | 0.267 | |
| dot-makeQCPlot | 5.101 | 0.047 | 5.210 | |
| extractSDRF | 0.149 | 0.010 | 0.160 | |
| getProcessed | 0.057 | 0.003 | 0.061 | |
| getSamplesInfo | 0.293 | 0.010 | 0.303 | |
| groupComparison | 0.220 | 0.006 | 0.226 | |
| groupComparisonPlots | 2.555 | 0.036 | 2.599 | |
| makePeptidesDictionary | 0.003 | 0.001 | 0.004 | |
| modelBasedQCPlots | 0.728 | 0.012 | 0.741 | |
| quantification | 0.171 | 0.006 | 0.177 | |