Sofie Van Gassen
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/FlowSOM |
| git_branch: RELEASE_3_17 |
| git_last_commit: 0b393bb |
| git_last_commit_date: 2023-04-25 10:36:54 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 727/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.8.0 (landing page) Sofie Van Gassen
| kjohnson2 | macOS 12.6.1 Monterey / 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: 2.8.0 |
| 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_2.8.0.tar.gz |
| StartedAt: 2023-10-17 20:07:57 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 20:21:53 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 835.5 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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/FlowSOM.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.8.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 ... NOTE
PlotManualBars: no visible binding for global variable ‘MC’
PlotManualBars: no visible binding for global variable ‘Manual’
Undefined global functions or variables:
MC Manual
* 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 56.417 1.413 84.530
PlotDimRed 49.583 1.265 74.046
PlotMarker 18.888 0.524 29.177
PlotOutliers 18.522 0.434 27.751
UpdateMetaclusters 18.209 0.480 27.370
PlotStars 15.628 0.409 24.389
GroupStats 13.509 0.455 21.364
FlowSOM 12.693 0.398 19.571
PlotGroups 12.135 0.371 18.172
AddAnnotation 9.764 0.311 15.273
QueryMultiple 9.589 0.242 14.840
query_multiple 9.516 0.252 14.828
Plot2DScatters 8.502 0.347 12.770
GetFlowJoLabels 8.289 0.354 12.842
PlotManualBars 8.266 0.257 12.080
PlotNode 7.436 0.238 11.596
PlotVariable 7.131 0.284 11.308
PlotNumbers 7.049 0.289 11.045
QueryStarPlot 7.146 0.178 11.102
PlotPies 6.831 0.261 10.645
UpdateNodeSize 6.521 0.128 8.697
CountGroups 6.270 0.242 9.873
PlotFlowSOM 5.959 0.258 9.390
GetFeatures 5.701 0.215 8.981
SaveClustersToFCS 5.579 0.296 8.940
MetaclusterMFIs 5.411 0.337 8.801
PlotLabels 5.469 0.206 7.041
NMetaclusters 5.157 0.329 8.127
NClusters 5.133 0.296 8.229
TestOutliers 4.955 0.221 7.654
GetMetaclusterCVs 4.811 0.251 6.497
PlotOverview2D 4.773 0.269 6.517
GetMFIs 4.569 0.274 6.799
GetMetaclusterMFIs 4.553 0.273 7.251
GetPercentages 4.537 0.264 7.305
MetaclusterCVs 4.536 0.254 7.229
GetMetaclusters 4.516 0.272 7.309
print.FlowSOM 4.547 0.239 7.176
GetMetaclusterPercentagesPositive 4.508 0.252 7.294
GetClusterMFIs 4.272 0.244 6.793
GetClusters 4.266 0.246 6.777
GetCounts 4.289 0.218 6.842
FlowSOMSubset 4.336 0.154 6.643
GetClusterPercentagesPositive 4.252 0.223 6.801
NewData 3.898 0.190 6.030
MetaClustering 3.686 0.226 5.951
ReadInput 3.681 0.170 5.987
metaClustering_consensus 3.269 0.160 5.170
* 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 NOTEs
See
‘/Users/biocbuild/bbs-3.17-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 14.0.0 (clang-1400.0.29.202)’ 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 -single_module -multiply_defined suppress -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 | 9.764 | 0.311 | 15.273 | |
| AggregateFlowFrames | 0.111 | 0.006 | 0.180 | |
| BuildMST | 1.411 | 0.039 | 2.208 | |
| BuildSOM | 1.398 | 0.048 | 2.202 | |
| CountGroups | 6.270 | 0.242 | 9.873 | |
| FMeasure | 0.001 | 0.000 | 0.003 | |
| FlowSOM | 12.693 | 0.398 | 19.571 | |
| FlowSOMSubset | 4.336 | 0.154 | 6.643 | |
| FlowSOMmary | 56.417 | 1.413 | 84.530 | |
| GetChannels | 0.044 | 0.004 | 0.070 | |
| GetClusterMFIs | 4.272 | 0.244 | 6.793 | |
| GetClusterPercentagesPositive | 4.252 | 0.223 | 6.801 | |
| GetClusters | 4.266 | 0.246 | 6.777 | |
| GetCounts | 4.289 | 0.218 | 6.842 | |
| GetFeatures | 5.701 | 0.215 | 8.981 | |
| GetFlowJoLabels | 8.289 | 0.354 | 12.842 | |
| GetMFIs | 4.569 | 0.274 | 6.799 | |
| GetMarkers | 0.044 | 0.002 | 0.057 | |
| GetMetaclusterCVs | 4.811 | 0.251 | 6.497 | |
| GetMetaclusterMFIs | 4.553 | 0.273 | 7.251 | |
| GetMetaclusterPercentagesPositive | 4.508 | 0.252 | 7.294 | |
| GetMetaclusters | 4.516 | 0.272 | 7.309 | |
| GetPercentages | 4.537 | 0.264 | 7.305 | |
| GroupStats | 13.509 | 0.455 | 21.364 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.007 | |
| Initialize_PCA | 0.001 | 0.000 | 0.003 | |
| MetaClustering | 3.686 | 0.226 | 5.951 | |
| MetaclusterCVs | 4.536 | 0.254 | 7.229 | |
| MetaclusterMFIs | 5.411 | 0.337 | 8.801 | |
| NClusters | 5.133 | 0.296 | 8.229 | |
| NMetaclusters | 5.157 | 0.329 | 8.127 | |
| NewData | 3.898 | 0.190 | 6.030 | |
| Plot2DScatters | 8.502 | 0.347 | 12.770 | |
| PlotCenters | 1.334 | 0.030 | 1.875 | |
| PlotClusters2D | 1.324 | 0.031 | 1.574 | |
| PlotDimRed | 49.583 | 1.265 | 74.046 | |
| PlotFileScatters | 0.922 | 0.022 | 1.448 | |
| PlotFlowSOM | 5.959 | 0.258 | 9.390 | |
| PlotGroups | 12.135 | 0.371 | 18.172 | |
| PlotLabels | 5.469 | 0.206 | 7.041 | |
| PlotManualBars | 8.266 | 0.257 | 12.080 | |
| PlotMarker | 18.888 | 0.524 | 29.177 | |
| PlotNode | 7.436 | 0.238 | 11.596 | |
| PlotNumbers | 7.049 | 0.289 | 11.045 | |
| PlotOutliers | 18.522 | 0.434 | 27.751 | |
| PlotOverview2D | 4.773 | 0.269 | 6.517 | |
| PlotPies | 6.831 | 0.261 | 10.645 | |
| PlotSD | 2.432 | 0.053 | 3.755 | |
| PlotStars | 15.628 | 0.409 | 24.389 | |
| PlotVariable | 7.131 | 0.284 | 11.308 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 9.589 | 0.242 | 14.840 | |
| QueryStarPlot | 7.146 | 0.178 | 11.102 | |
| ReadInput | 3.681 | 0.170 | 5.987 | |
| SaveClustersToFCS | 5.579 | 0.296 | 8.940 | |
| TestOutliers | 4.955 | 0.221 | 7.654 | |
| UpdateMetaclusters | 18.209 | 0.480 | 27.370 | |
| UpdateNodeSize | 6.521 | 0.128 | 8.697 | |
| get_channels | 0.046 | 0.003 | 0.085 | |
| get_markers | 0.046 | 0.002 | 0.069 | |
| metaClustering_consensus | 3.269 | 0.160 | 5.170 | |
| plotStarLegend | 0.435 | 0.007 | 0.684 | |
| print.FlowSOM | 4.547 | 0.239 | 7.176 | |
| query_multiple | 9.516 | 0.252 | 14.828 | |