Sofie Van Gassen
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 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 2024-03-28 11:32:20 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| 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 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: 2024-03-27 13:32:25 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 13:43:16 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 650.4 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_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* 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 67.965 2.863 71.460
PlotDimRed 49.555 3.094 53.138
PlotMarker 23.884 1.199 25.258
UpdateMetaclusters 23.067 1.356 24.484
PlotStars 18.972 1.259 20.342
GroupStats 15.522 1.094 16.746
PlotOutliers 15.476 0.697 16.301
FlowSOM 14.709 0.997 16.018
QueryMultiple 14.565 0.549 15.141
query_multiple 14.366 0.530 15.030
PlotGroups 13.123 1.109 14.316
AddAnnotation 11.481 0.638 12.169
Plot2DScatters 11.333 0.729 12.194
QueryStarPlot 10.416 0.445 10.904
PlotNode 8.881 0.680 9.613
PlotVariable 8.694 0.764 9.495
GetFlowJoLabels 8.732 0.721 9.544
PlotNumbers 8.515 0.653 9.203
PlotManualBars 8.228 0.787 9.058
UpdateNodeSize 8.470 0.257 8.734
PlotPies 7.932 0.741 8.693
CountGroups 7.147 0.634 7.925
PlotFlowSOM 6.691 1.060 7.848
SaveClustersToFCS 5.951 0.910 6.891
PlotLabels 6.354 0.501 6.883
MetaclusterMFIs 5.586 1.085 6.734
NMetaclusters 5.466 0.630 6.154
GetMetaclusters 5.349 0.742 6.134
GetMFIs 5.081 0.936 6.062
NClusters 5.157 0.828 6.104
GetFeatures 5.507 0.448 6.007
TestOutliers 5.404 0.537 5.958
PlotOverview2D 5.204 0.667 5.915
print.FlowSOM 5.141 0.720 5.926
GetPercentages 5.016 0.808 5.863
GetClusterMFIs 4.961 0.669 5.635
MetaclusterCVs 4.956 0.648 5.647
GetMetaclusterCVs 4.891 0.521 5.431
GetMetaclusterMFIs 4.839 0.534 5.416
GetClusterPercentagesPositive 4.598 0.746 5.360
GetClusters 4.542 0.796 5.353
GetCounts 4.667 0.530 5.218
GetMetaclusterPercentagesPositive 4.549 0.449 5.031
* 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 | 11.481 | 0.638 | 12.169 | |
| AggregateFlowFrames | 0.094 | 0.006 | 0.100 | |
| BuildMST | 1.491 | 0.095 | 1.587 | |
| BuildSOM | 1.546 | 0.117 | 1.669 | |
| CountGroups | 7.147 | 0.634 | 7.925 | |
| FMeasure | 0.002 | 0.000 | 0.002 | |
| FlowSOM | 14.709 | 0.997 | 16.018 | |
| FlowSOMSubset | 4.379 | 0.411 | 4.814 | |
| FlowSOMmary | 67.965 | 2.863 | 71.460 | |
| GetChannels | 0.040 | 0.003 | 0.043 | |
| GetClusterMFIs | 4.961 | 0.669 | 5.635 | |
| GetClusterPercentagesPositive | 4.598 | 0.746 | 5.360 | |
| GetClusters | 4.542 | 0.796 | 5.353 | |
| GetCounts | 4.667 | 0.530 | 5.218 | |
| GetFeatures | 5.507 | 0.448 | 6.007 | |
| GetFlowJoLabels | 8.732 | 0.721 | 9.544 | |
| GetMFIs | 5.081 | 0.936 | 6.062 | |
| GetMarkers | 0.040 | 0.006 | 0.046 | |
| GetMetaclusterCVs | 4.891 | 0.521 | 5.431 | |
| GetMetaclusterMFIs | 4.839 | 0.534 | 5.416 | |
| GetMetaclusterPercentagesPositive | 4.549 | 0.449 | 5.031 | |
| GetMetaclusters | 5.349 | 0.742 | 6.134 | |
| GetPercentages | 5.016 | 0.808 | 5.863 | |
| GroupStats | 15.522 | 1.094 | 16.746 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.004 | |
| Initialize_PCA | 0.001 | 0.001 | 0.002 | |
| MetaClustering | 3.229 | 0.480 | 3.743 | |
| MetaclusterCVs | 4.956 | 0.648 | 5.647 | |
| MetaclusterMFIs | 5.586 | 1.085 | 6.734 | |
| NClusters | 5.157 | 0.828 | 6.104 | |
| NMetaclusters | 5.466 | 0.630 | 6.154 | |
| NewData | 4.148 | 0.481 | 4.665 | |
| Plot2DScatters | 11.333 | 0.729 | 12.194 | |
| PlotCenters | 1.292 | 0.170 | 1.484 | |
| PlotClusters2D | 1.283 | 0.203 | 1.508 | |
| PlotDimRed | 49.555 | 3.094 | 53.138 | |
| PlotFileScatters | 1.015 | 0.043 | 1.072 | |
| PlotFlowSOM | 6.691 | 1.060 | 7.848 | |
| PlotGroups | 13.123 | 1.109 | 14.316 | |
| PlotLabels | 6.354 | 0.501 | 6.883 | |
| PlotManualBars | 8.228 | 0.787 | 9.058 | |
| PlotMarker | 23.884 | 1.199 | 25.258 | |
| PlotNode | 8.881 | 0.680 | 9.613 | |
| PlotNumbers | 8.515 | 0.653 | 9.203 | |
| PlotOutliers | 15.476 | 0.697 | 16.301 | |
| PlotOverview2D | 5.204 | 0.667 | 5.915 | |
| PlotPies | 7.932 | 0.741 | 8.693 | |
| PlotSD | 2.891 | 0.121 | 3.025 | |
| PlotStars | 18.972 | 1.259 | 20.342 | |
| PlotVariable | 8.694 | 0.764 | 9.495 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 14.565 | 0.549 | 15.141 | |
| QueryStarPlot | 10.416 | 0.445 | 10.904 | |
| ReadInput | 3.848 | 0.524 | 4.389 | |
| SaveClustersToFCS | 5.951 | 0.910 | 6.891 | |
| TestOutliers | 5.404 | 0.537 | 5.958 | |
| UpdateMetaclusters | 23.067 | 1.356 | 24.484 | |
| UpdateNodeSize | 8.470 | 0.257 | 8.734 | |
| get_channels | 0.042 | 0.005 | 0.046 | |
| get_markers | 0.037 | 0.003 | 0.040 | |
| metaClustering_consensus | 2.741 | 0.261 | 3.011 | |
| plotStarLegend | 0.919 | 0.010 | 0.929 | |
| print.FlowSOM | 5.141 | 0.720 | 5.926 | |
| query_multiple | 14.366 | 0.530 | 15.030 | |