Sofie Van Gassen
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/FlowSOM |
| git_branch: RELEASE_3_18 |
| git_last_commit: 36b3305 |
| git_last_commit_date: 2023-10-24 10:40:45 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:10 -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 738/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.10.0 (landing page) Sofie Van Gassen
| kjohnson1 | macOS 13.6.1 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: 2.10.0 |
| 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_2.10.0.tar.gz |
| StartedAt: 2024-04-17 13:59:00 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 14:10:02 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 661.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### 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_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/FlowSOM.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 ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.10.0’
* 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-1500.0.40.1)’
* 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 ... 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 ... 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 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 69.209 2.871 72.706
PlotDimRed 51.137 4.139 55.848
PlotMarker 23.912 1.206 25.180
UpdateMetaclusters 22.690 1.374 24.094
PlotStars 18.780 1.108 19.993
GroupStats 16.011 0.968 17.153
PlotOutliers 15.973 0.869 16.933
query_multiple 14.873 0.550 15.450
QueryMultiple 14.811 0.520 15.350
FlowSOM 14.393 0.807 15.263
PlotGroups 13.443 1.148 14.652
AddAnnotation 12.082 0.731 13.099
Plot2DScatters 10.422 0.645 11.318
QueryStarPlot 10.382 0.384 10.775
GetFlowJoLabels 9.261 0.807 10.154
PlotVariable 8.644 0.785 9.441
PlotNode 8.212 0.985 9.238
PlotNumbers 8.409 0.686 9.139
PlotPies 8.418 0.630 9.069
UpdateNodeSize 8.439 0.243 8.721
PlotManualBars 7.674 0.892 8.637
PlotFlowSOM 7.395 0.858 8.300
CountGroups 6.980 0.794 7.958
NMetaclusters 6.085 1.246 7.398
TestOutliers 5.938 0.751 6.762
SaveClustersToFCS 5.867 0.683 6.597
GetMetaclusterMFIs 5.436 1.033 6.525
PlotLabels 5.849 0.605 6.470
GetFeatures 5.719 0.681 6.527
MetaclusterMFIs 5.644 0.707 6.412
NClusters 5.548 0.726 6.332
MetaclusterCVs 5.508 0.729 6.292
GetMFIs 5.576 0.651 6.374
GetMetaclusterCVs 5.067 0.818 5.981
print.FlowSOM 5.015 0.703 5.730
GetMetaclusters 4.887 0.770 5.719
GetMetaclusterPercentagesPositive 4.895 0.731 5.762
GetPercentages 4.937 0.674 5.650
PlotOverview2D 4.880 0.601 5.514
GetClusterMFIs 4.772 0.629 5.545
GetClusterPercentagesPositive 4.663 0.704 5.371
GetCounts 4.621 0.651 5.325
GetClusters 4.569 0.654 5.228
NewData 4.270 0.685 5.016
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.18-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/4.3-arm64/Resources/library’ * installing *source* package ‘FlowSOM’ ... ** 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 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/4.3-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 | 12.082 | 0.731 | 13.099 | |
| AggregateFlowFrames | 0.095 | 0.010 | 0.105 | |
| BuildMST | 1.513 | 0.086 | 1.674 | |
| BuildSOM | 1.572 | 0.082 | 1.670 | |
| CountGroups | 6.980 | 0.794 | 7.958 | |
| FMeasure | 0.002 | 0.001 | 0.002 | |
| FlowSOM | 14.393 | 0.807 | 15.263 | |
| FlowSOMSubset | 4.660 | 0.314 | 4.987 | |
| FlowSOMmary | 69.209 | 2.871 | 72.706 | |
| GetChannels | 0.040 | 0.004 | 0.044 | |
| GetClusterMFIs | 4.772 | 0.629 | 5.545 | |
| GetClusterPercentagesPositive | 4.663 | 0.704 | 5.371 | |
| GetClusters | 4.569 | 0.654 | 5.228 | |
| GetCounts | 4.621 | 0.651 | 5.325 | |
| GetFeatures | 5.719 | 0.681 | 6.527 | |
| GetFlowJoLabels | 9.261 | 0.807 | 10.154 | |
| GetMFIs | 5.576 | 0.651 | 6.374 | |
| GetMarkers | 0.040 | 0.003 | 0.045 | |
| GetMetaclusterCVs | 5.067 | 0.818 | 5.981 | |
| GetMetaclusterMFIs | 5.436 | 1.033 | 6.525 | |
| GetMetaclusterPercentagesPositive | 4.895 | 0.731 | 5.762 | |
| GetMetaclusters | 4.887 | 0.770 | 5.719 | |
| GetPercentages | 4.937 | 0.674 | 5.650 | |
| GroupStats | 16.011 | 0.968 | 17.153 | |
| Initialize_KWSP | 0.004 | 0.001 | 0.004 | |
| Initialize_PCA | 0.001 | 0.000 | 0.001 | |
| MetaClustering | 3.075 | 0.845 | 3.979 | |
| MetaclusterCVs | 5.508 | 0.729 | 6.292 | |
| MetaclusterMFIs | 5.644 | 0.707 | 6.412 | |
| NClusters | 5.548 | 0.726 | 6.332 | |
| NMetaclusters | 6.085 | 1.246 | 7.398 | |
| NewData | 4.270 | 0.685 | 5.016 | |
| Plot2DScatters | 10.422 | 0.645 | 11.318 | |
| PlotCenters | 1.384 | 0.123 | 1.513 | |
| PlotClusters2D | 1.301 | 0.117 | 1.453 | |
| PlotDimRed | 51.137 | 4.139 | 55.848 | |
| PlotFileScatters | 0.967 | 0.022 | 0.989 | |
| PlotFlowSOM | 7.395 | 0.858 | 8.300 | |
| PlotGroups | 13.443 | 1.148 | 14.652 | |
| PlotLabels | 5.849 | 0.605 | 6.470 | |
| PlotManualBars | 7.674 | 0.892 | 8.637 | |
| PlotMarker | 23.912 | 1.206 | 25.180 | |
| PlotNode | 8.212 | 0.985 | 9.238 | |
| PlotNumbers | 8.409 | 0.686 | 9.139 | |
| PlotOutliers | 15.973 | 0.869 | 16.933 | |
| PlotOverview2D | 4.880 | 0.601 | 5.514 | |
| PlotPies | 8.418 | 0.630 | 9.069 | |
| PlotSD | 2.919 | 0.117 | 3.050 | |
| PlotStars | 18.780 | 1.108 | 19.993 | |
| PlotVariable | 8.644 | 0.785 | 9.441 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 14.811 | 0.520 | 15.350 | |
| QueryStarPlot | 10.382 | 0.384 | 10.775 | |
| ReadInput | 3.213 | 0.498 | 3.722 | |
| SaveClustersToFCS | 5.867 | 0.683 | 6.597 | |
| TestOutliers | 5.938 | 0.751 | 6.762 | |
| UpdateMetaclusters | 22.690 | 1.374 | 24.094 | |
| UpdateNodeSize | 8.439 | 0.243 | 8.721 | |
| get_channels | 0.058 | 0.006 | 0.063 | |
| get_markers | 0.041 | 0.003 | 0.044 | |
| metaClustering_consensus | 2.584 | 0.289 | 2.896 | |
| plotStarLegend | 0.779 | 0.010 | 0.815 | |
| print.FlowSOM | 5.015 | 0.703 | 5.730 | |
| query_multiple | 14.873 | 0.550 | 15.450 | |