Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:34 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 750/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.12.0 (landing page) Sofie Van Gassen
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the FlowSOM 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: FlowSOM |
Version: 2.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.12.0.tar.gz |
StartedAt: 2024-05-06 21:35:25 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 21:38:43 -0400 (Mon, 06 May 2024) |
EllapsedTime: 198.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FlowSOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/FlowSOM.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.12.0’ * 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 ‘FlowSOM’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) PlotDimRed.Rd:55: Lost braces 55 | of the dimred default = function(dimred){dimred$Y}.} | ^ * 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 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 FlowSOMmary 19.039 0.903 19.838 PlotDimRed 16.219 1.160 17.385 PlotMarker 6.639 0.524 7.166 UpdateMetaclusters 5.976 0.473 6.451 PlotOutliers 5.417 0.261 5.685 PlotStars 5.134 0.403 5.545 * 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 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/FlowSOM.Rcheck/00check.log’ for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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 som.c -o som.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 FlowSOM.so som.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-FlowSOM/00new/FlowSOM/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 (FlowSOM)
FlowSOM.Rcheck/FlowSOM-Ex.timings
name | user | system | elapsed | |
AddAnnotation | 2.886 | 0.092 | 2.978 | |
AggregateFlowFrames | 0.031 | 0.003 | 0.034 | |
BuildMST | 0.534 | 0.032 | 0.566 | |
BuildSOM | 0.495 | 0.029 | 0.525 | |
CountGroups | 2.011 | 0.124 | 2.140 | |
FMeasure | 0.000 | 0.000 | 0.001 | |
FlowSOM | 4.290 | 0.259 | 4.549 | |
FlowSOMSubset | 1.488 | 0.107 | 1.598 | |
FlowSOMmary | 19.039 | 0.903 | 19.838 | |
GetChannels | 0.013 | 0.002 | 0.016 | |
GetClusterMFIs | 1.556 | 0.268 | 1.825 | |
GetClusterPercentagesPositive | 1.560 | 0.254 | 1.814 | |
GetClusters | 1.552 | 0.236 | 1.793 | |
GetCounts | 1.546 | 0.251 | 1.799 | |
GetFeatures | 1.837 | 0.147 | 1.989 | |
GetFlowJoLabels | 2.777 | 0.277 | 3.060 | |
GetMFIs | 1.638 | 0.233 | 1.871 | |
GetMarkers | 0.013 | 0.001 | 0.015 | |
GetMetaclusterCVs | 1.809 | 0.246 | 2.055 | |
GetMetaclusterMFIs | 1.662 | 0.234 | 1.897 | |
GetMetaclusterPercentagesPositive | 1.580 | 0.293 | 1.873 | |
GetMetaclusters | 1.566 | 0.259 | 1.827 | |
GetPercentages | 1.702 | 0.282 | 1.985 | |
GroupStats | 4.349 | 0.330 | 4.689 | |
Initialize_KWSP | 0.001 | 0.000 | 0.001 | |
Initialize_PCA | 0 | 0 | 0 | |
MetaClustering | 1.081 | 0.173 | 1.256 | |
MetaclusterCVs | 1.617 | 0.234 | 1.854 | |
MetaclusterMFIs | 1.800 | 0.302 | 2.105 | |
NClusters | 1.820 | 0.302 | 2.122 | |
NMetaclusters | 2.106 | 0.412 | 2.520 | |
NewData | 1.512 | 0.197 | 1.709 | |
Plot2DScatters | 2.753 | 0.333 | 3.096 | |
PlotCenters | 0.424 | 0.076 | 0.501 | |
PlotClusters2D | 0.409 | 0.073 | 0.482 | |
PlotDimRed | 16.219 | 1.160 | 17.385 | |
PlotFileScatters | 0.237 | 0.008 | 0.245 | |
PlotFlowSOM | 2.148 | 0.270 | 2.426 | |
PlotGroups | 3.972 | 0.381 | 4.353 | |
PlotLabels | 1.995 | 0.207 | 2.205 | |
PlotManualBars | 2.514 | 0.292 | 2.808 | |
PlotMarker | 6.639 | 0.524 | 7.166 | |
PlotNode | 2.528 | 0.302 | 2.839 | |
PlotNumbers | 2.405 | 0.329 | 2.736 | |
PlotOutliers | 5.417 | 0.261 | 5.685 | |
PlotOverview2D | 2.035 | 0.285 | 2.340 | |
PlotPies | 2.534 | 0.368 | 2.903 | |
PlotSD | 0.779 | 0.062 | 0.846 | |
PlotStars | 5.134 | 0.403 | 5.545 | |
PlotVariable | 2.300 | 0.266 | 2.568 | |
Purity | 0.001 | 0.000 | 0.000 | |
QueryMultiple | 3.199 | 0.160 | 3.361 | |
QueryStarPlot | 2.543 | 0.150 | 2.694 | |
ReadInput | 1.065 | 0.108 | 1.176 | |
SaveClustersToFCS | 1.983 | 0.332 | 2.316 | |
TestOutliers | 1.993 | 0.293 | 2.287 | |
UpdateMetaclusters | 5.976 | 0.473 | 6.451 | |
UpdateNodeSize | 2.082 | 0.086 | 2.173 | |
get_channels | 0.014 | 0.001 | 0.014 | |
get_markers | 0.013 | 0.001 | 0.015 | |
metaClustering_consensus | 0.951 | 0.116 | 1.067 | |
plotStarLegend | 0.165 | 0.003 | 0.167 | |
print.FlowSOM | 1.683 | 0.266 | 1.953 | |
query_multiple | 3.218 | 0.165 | 3.387 | |