Sofie Van Gassen
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 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 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:21 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the FlowSOM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FlowSOM.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 2024-03-03 20:40:26 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 20:51:45 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 679.2 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/meat/FlowSOM.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 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 ... 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 63.913 2.899 67.407
PlotDimRed 42.362 2.926 45.952
PlotMarker 27.771 1.748 29.881
UpdateMetaclusters 24.129 2.004 26.684
PlotStars 20.097 1.452 21.803
PlotOutliers 20.389 1.138 21.765
GroupStats 17.450 1.251 18.906
PlotGroups 15.391 1.681 17.330
query_multiple 16.200 0.746 17.143
QueryMultiple 15.831 0.737 16.734
FlowSOM 14.604 1.262 16.079
Plot2DScatters 12.443 1.036 13.633
AddAnnotation 12.423 0.763 13.337
QueryStarPlot 10.919 0.519 11.573
PlotNumbers 9.031 1.016 10.191
PlotNode 8.638 1.106 9.865
PlotVariable 8.540 1.167 9.842
PlotPies 8.426 1.175 9.925
GetFlowJoLabels 8.669 0.790 9.568
UpdateNodeSize 9.071 0.332 9.520
PlotManualBars 8.238 1.048 9.399
PlotFlowSOM 7.415 1.035 8.569
CountGroups 6.468 0.788 7.454
PlotLabels 6.056 0.777 6.926
NMetaclusters 5.678 1.099 6.943
SaveClustersToFCS 5.376 1.228 6.723
NClusters 5.487 1.027 6.636
GetFeatures 5.908 0.501 6.492
MetaclusterMFIs 5.503 0.894 6.495
MetaclusterCVs 5.214 0.780 6.069
GetPercentages 4.936 0.885 5.934
print.FlowSOM 4.782 0.986 5.904
GetMetaclusterMFIs 4.913 0.854 5.857
PlotOverview2D 4.899 0.865 5.964
TestOutliers 4.959 0.794 5.835
GetMFIs 4.747 0.760 5.615
GetMetaclusters 4.676 0.827 5.615
GetMetaclusterPercentagesPositive 4.639 0.785 5.517
GetMetaclusterCVs 4.633 0.783 5.508
GetCounts 4.423 0.701 5.201
GetClusterPercentagesPositive 4.366 0.722 5.275
NewData 4.347 0.599 5.018
GetClusterMFIs 4.349 0.597 5.019
* 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/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-x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c som.c -o som.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 | 12.423 | 0.763 | 13.337 | |
| AggregateFlowFrames | 0.108 | 0.008 | 0.119 | |
| BuildMST | 1.530 | 0.107 | 1.666 | |
| BuildSOM | 1.664 | 0.128 | 1.852 | |
| CountGroups | 6.468 | 0.788 | 7.454 | |
| FMeasure | 0.002 | 0.000 | 0.003 | |
| FlowSOM | 14.604 | 1.262 | 16.079 | |
| FlowSOMSubset | 4.365 | 0.483 | 4.914 | |
| FlowSOMmary | 63.913 | 2.899 | 67.407 | |
| GetChannels | 0.043 | 0.005 | 0.049 | |
| GetClusterMFIs | 4.349 | 0.597 | 5.019 | |
| GetClusterPercentagesPositive | 4.366 | 0.722 | 5.275 | |
| GetClusters | 4.301 | 0.614 | 4.978 | |
| GetCounts | 4.423 | 0.701 | 5.201 | |
| GetFeatures | 5.908 | 0.501 | 6.492 | |
| GetFlowJoLabels | 8.669 | 0.790 | 9.568 | |
| GetMFIs | 4.747 | 0.760 | 5.615 | |
| GetMarkers | 0.046 | 0.005 | 0.054 | |
| GetMetaclusterCVs | 4.633 | 0.783 | 5.508 | |
| GetMetaclusterMFIs | 4.913 | 0.854 | 5.857 | |
| GetMetaclusterPercentagesPositive | 4.639 | 0.785 | 5.517 | |
| GetMetaclusters | 4.676 | 0.827 | 5.615 | |
| GetPercentages | 4.936 | 0.885 | 5.934 | |
| GroupStats | 17.450 | 1.251 | 18.906 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.005 | |
| Initialize_PCA | 0.001 | 0.001 | 0.001 | |
| MetaClustering | 3.335 | 0.725 | 4.132 | |
| MetaclusterCVs | 5.214 | 0.780 | 6.069 | |
| MetaclusterMFIs | 5.503 | 0.894 | 6.495 | |
| NClusters | 5.487 | 1.027 | 6.636 | |
| NMetaclusters | 5.678 | 1.099 | 6.943 | |
| NewData | 4.347 | 0.599 | 5.018 | |
| Plot2DScatters | 12.443 | 1.036 | 13.633 | |
| PlotCenters | 1.339 | 0.171 | 1.527 | |
| PlotClusters2D | 1.324 | 0.126 | 1.462 | |
| PlotDimRed | 42.362 | 2.926 | 45.952 | |
| PlotFileScatters | 1.163 | 0.052 | 1.228 | |
| PlotFlowSOM | 7.415 | 1.035 | 8.569 | |
| PlotGroups | 15.391 | 1.681 | 17.330 | |
| PlotLabels | 6.056 | 0.777 | 6.926 | |
| PlotManualBars | 8.238 | 1.048 | 9.399 | |
| PlotMarker | 27.771 | 1.748 | 29.881 | |
| PlotNode | 8.638 | 1.106 | 9.865 | |
| PlotNumbers | 9.031 | 1.016 | 10.191 | |
| PlotOutliers | 20.389 | 1.138 | 21.765 | |
| PlotOverview2D | 4.899 | 0.865 | 5.964 | |
| PlotPies | 8.426 | 1.175 | 9.925 | |
| PlotSD | 3.056 | 0.189 | 3.291 | |
| PlotStars | 20.097 | 1.452 | 21.803 | |
| PlotVariable | 8.540 | 1.167 | 9.842 | |
| Purity | 0.001 | 0.001 | 0.001 | |
| QueryMultiple | 15.831 | 0.737 | 16.734 | |
| QueryStarPlot | 10.919 | 0.519 | 11.573 | |
| ReadInput | 3.641 | 0.805 | 4.548 | |
| SaveClustersToFCS | 5.376 | 1.228 | 6.723 | |
| TestOutliers | 4.959 | 0.794 | 5.835 | |
| UpdateMetaclusters | 24.129 | 2.004 | 26.684 | |
| UpdateNodeSize | 9.071 | 0.332 | 9.520 | |
| get_channels | 0.047 | 0.004 | 0.054 | |
| get_markers | 0.061 | 0.012 | 0.075 | |
| metaClustering_consensus | 2.746 | 0.711 | 3.538 | |
| plotStarLegend | 1.006 | 0.018 | 1.036 | |
| print.FlowSOM | 4.782 | 0.986 | 5.904 | |
| query_multiple | 16.200 | 0.746 | 17.143 | |