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This page was generated on 2024-05-13 11:32:04 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 702/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.61.0 (landing page) Mark Robinson
| kjohnson1 | macOS 13.6.6 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: 1.61.0 |
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_1.61.0.tar.gz |
StartedAt: 2024-05-12 13:38:24 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 13:54:21 -0400 (Sun, 12 May 2024) |
EllapsedTime: 957.2 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_1.61.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/flagme.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.61.0’ * 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 code 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 whether 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 Rd file 'addXCMSPeaks.Rd': ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’ ‘[xcms]{peaksDataset}’ Missing link or links in Rd file 'plotAlignment-peaksAlignment-method.Rd': ‘plotAlignment’ Missing link or links in Rd file '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 109.864 16.192 69.693 addXCMSPeaks 61.353 7.807 51.189 retFatMatrix 56.774 8.415 45.646 plotFrags 55.296 8.646 44.312 peaksAlignment-class 55.469 7.921 44.765 corPrt 54.328 8.138 44.047 plotAlignment-peaksAlignment-method 54.317 8.124 43.403 progressiveAlignment-class 53.634 8.431 43.200 ndpRT 52.830 8.304 41.968 dynRT 51.967 8.275 42.460 imputePeaks 12.953 0.268 13.297 plotChrom-peaksDataset-method 10.743 0.225 11.020 rmaFitUnit 9.391 0.306 9.769 calcTimeDiffs 9.427 0.263 10.434 multipleAlignment-class 9.190 0.194 9.407 gatherInfo 9.095 0.188 9.317 clusterAlignment 8.199 0.142 8.912 dp 7.726 0.192 8.575 addAMDISPeaks 7.187 0.140 7.390 plotClustAlignment-clusterAlignment-method 6.837 0.136 7.032 peaksDataset 6.586 0.186 6.801 normDotProduct 6.278 0.147 6.498 plotImage 5.683 0.121 5.830 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-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/4.4-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/4.4-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 | 7.187 | 0.140 | 7.390 | |
addChromaTOFPeaks | 3.822 | 0.092 | 4.022 | |
addXCMSPeaks | 61.353 | 7.807 | 51.189 | |
betweenAlignment | 0.000 | 0.000 | 0.001 | |
calcTimeDiffs | 9.427 | 0.263 | 10.434 | |
clusterAlignment | 8.199 | 0.142 | 8.912 | |
corPrt | 54.328 | 8.138 | 44.047 | |
dp | 7.726 | 0.192 | 8.575 | |
dynRT | 51.967 | 8.275 | 42.460 | |
gatherInfo | 9.095 | 0.188 | 9.317 | |
imputePeaks | 12.953 | 0.268 | 13.297 | |
multipleAlignment-class | 9.190 | 0.194 | 9.407 | |
ndpRT | 52.830 | 8.304 | 41.968 | |
normDotProduct | 6.278 | 0.147 | 6.498 | |
parseChromaTOF | 2.289 | 0.039 | 2.339 | |
parseELU | 1.805 | 0.012 | 1.850 | |
peaksAlignment-class | 55.469 | 7.921 | 44.765 | |
peaksDataset | 6.586 | 0.186 | 6.801 | |
plotAlignedFrags | 109.864 | 16.192 | 69.693 | |
plotAlignment-peaksAlignment-method | 54.317 | 8.124 | 43.403 | |
plotChrom-peaksDataset-method | 10.743 | 0.225 | 11.020 | |
plotClustAlignment-clusterAlignment-method | 6.837 | 0.136 | 7.032 | |
plotFrags | 55.296 | 8.646 | 44.312 | |
plotImage | 5.683 | 0.121 | 5.830 | |
progressiveAlignment-class | 53.634 | 8.431 | 43.200 | |
retFatMatrix | 56.774 | 8.415 | 45.646 | |
rmaFitUnit | 9.391 | 0.306 | 9.769 | |