Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-03-28 11:32:20 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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 715/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.58.0 (landing page) Mark Robinson
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the flagme 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: flagme |
Version: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.58.0.tar.gz |
StartedAt: 2024-03-27 13:21:26 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 13:36:15 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 889.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/flagme.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 ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.58.0’ * 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 ‘flagme’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 Unexported object imported by a ':::' call: ‘xcms:::rectUnique’ 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 addXCMSPeaks: no visible global function definition for ‘bpparam’ addXCMSPeaks: no visible global function definition for ‘sampnames’ addXCMSPeaks : <anonymous> : <anonymous>: no visible global function definition for ‘setNames’ importSpec : <anonymous>: no visible global function definition for ‘setNames’ Undefined global functions or variables: bpparam sampnames setNames Consider adding importFrom("stats", "setNames") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'addXCMSPeaks.Rd': ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’ ‘[xcms]{peaksDataset}’ Missing link or links in documentation object 'plotAlignment-peaksAlignment-method.Rd': ‘plotAlignment’ Missing link or links in documentation object 'plotClustAlignment-clusterAlignment-method.Rd': ‘plotAlignment’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’ Undocumented S4 methods: generic 'show' and siglist 'betweenAlignment' All user-level objects in a package (including S4 classes and methods) 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotAlignedFrags 98.992 17.397 63.076 addXCMSPeaks 56.643 8.229 47.103 dynRT 51.320 9.053 40.782 plotAlignment-peaksAlignment-method 49.923 9.610 40.992 corPrt 50.064 9.144 42.193 ndpRT 48.132 9.385 39.755 peaksAlignment-class 48.889 8.378 39.108 retFatMatrix 45.366 9.804 38.755 progressiveAlignment-class 44.554 9.131 37.518 plotFrags 44.205 9.055 37.130 imputePeaks 10.268 0.331 10.642 plotChrom-peaksDataset-method 8.279 0.354 8.663 rmaFitUnit 7.445 0.478 7.930 calcTimeDiffs 7.370 0.421 7.844 gatherInfo 7.368 0.285 7.678 multipleAlignment-class 7.194 0.180 7.406 clusterAlignment 6.306 0.262 6.630 plotClustAlignment-clusterAlignment-method 6.285 0.258 6.581 addAMDISPeaks 6.347 0.155 6.542 dp 6.290 0.196 6.666 normDotProduct 6.249 0.199 6.456 peaksDataset 5.980 0.301 6.350 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/flagme.Rcheck/00check.log’ for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘flagme’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dp.c -o dp.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pearson.c -o pearson.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-flagme/00new/flagme/libs ** R ** 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 (flagme)
flagme.Rcheck/flagme-Ex.timings
name | user | system | elapsed | |
addAMDISPeaks | 6.347 | 0.155 | 6.542 | |
addChromaTOFPeaks | 3.951 | 0.161 | 4.264 | |
addXCMSPeaks | 56.643 | 8.229 | 47.103 | |
betweenAlignment | 0.000 | 0.000 | 0.001 | |
calcTimeDiffs | 7.370 | 0.421 | 7.844 | |
clusterAlignment | 6.306 | 0.262 | 6.630 | |
corPrt | 50.064 | 9.144 | 42.193 | |
dp | 6.290 | 0.196 | 6.666 | |
dynRT | 51.320 | 9.053 | 40.782 | |
gatherInfo | 7.368 | 0.285 | 7.678 | |
imputePeaks | 10.268 | 0.331 | 10.642 | |
multipleAlignment-class | 7.194 | 0.180 | 7.406 | |
ndpRT | 48.132 | 9.385 | 39.755 | |
normDotProduct | 6.249 | 0.199 | 6.456 | |
parseChromaTOF | 2.125 | 0.025 | 2.156 | |
parseELU | 1.722 | 0.010 | 1.756 | |
peaksAlignment-class | 48.889 | 8.378 | 39.108 | |
peaksDataset | 5.980 | 0.301 | 6.350 | |
plotAlignedFrags | 98.992 | 17.397 | 63.076 | |
plotAlignment-peaksAlignment-method | 49.923 | 9.610 | 40.992 | |
plotChrom-peaksDataset-method | 8.279 | 0.354 | 8.663 | |
plotClustAlignment-clusterAlignment-method | 6.285 | 0.258 | 6.581 | |
plotFrags | 44.205 | 9.055 | 37.130 | |
plotImage | 3.509 | 0.134 | 3.665 | |
progressiveAlignment-class | 44.554 | 9.131 | 37.518 | |
retFatMatrix | 45.366 | 9.804 | 38.755 | |
rmaFitUnit | 7.445 | 0.478 | 7.930 | |