Sofie Van Gassen
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 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 Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:44 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 | | ||||||||
| merida1 | 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: 2024-03-28 02:54:49 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:15:07 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 1218.5 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/meat/FlowSOM.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 12.7.1
* 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 114.350 2.665 123.838
PlotDimRed 74.971 2.511 83.362
PlotMarker 50.387 1.131 58.292
UpdateMetaclusters 45.108 1.185 50.959
PlotStars 37.324 0.958 41.235
PlotOutliers 36.231 0.792 39.936
GroupStats 33.275 1.057 40.704
QueryMultiple 29.020 0.559 32.062
query_multiple 28.803 0.485 29.911
PlotGroups 28.177 0.954 31.749
FlowSOM 26.086 1.012 29.497
Plot2DScatters 22.072 0.739 23.606
AddAnnotation 22.054 0.745 24.127
QueryStarPlot 20.149 0.414 22.114
UpdateNodeSize 18.383 0.275 20.601
PlotNumbers 16.420 0.630 18.026
PlotNode 15.975 0.690 17.976
GetFlowJoLabels 15.755 0.625 17.292
PlotVariable 15.121 0.668 17.654
PlotManualBars 14.906 0.661 16.525
PlotPies 13.328 0.693 15.071
PlotFlowSOM 12.128 0.681 13.851
GetFeatures 11.880 0.384 13.063
CountGroups 11.081 0.595 12.374
PlotLabels 10.597 0.606 11.877
SaveClustersToFCS 9.630 0.725 11.608
NClusters 9.450 0.741 10.704
NMetaclusters 9.071 0.838 10.381
MetaclusterMFIs 9.054 0.699 10.282
TestOutliers 8.614 0.532 10.045
FlowSOMSubset 8.401 0.393 9.789
GetMetaclusterMFIs 8.183 0.596 9.351
GetMFIs 8.030 0.662 9.612
MetaclusterCVs 8.012 0.588 9.357
GetMetaclusters 7.832 0.694 10.785
PlotOverview2D 7.959 0.560 9.040
GetMetaclusterCVs 7.912 0.548 9.295
GetMetaclusterPercentagesPositive 7.865 0.555 9.143
print.FlowSOM 7.606 0.782 8.485
GetPercentages 7.724 0.616 11.860
GetCounts 7.472 0.496 8.364
GetClusterPercentagesPositive 7.485 0.480 8.319
GetClusterMFIs 7.440 0.476 8.587
GetClusters 7.395 0.441 8.256
NewData 7.342 0.484 8.354
ReadInput 6.607 0.488 7.928
MetaClustering 6.404 0.491 7.320
metaClustering_consensus 5.310 0.360 5.848
PlotSD 5.373 0.190 6.100
* 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 | 22.054 | 0.745 | 24.127 | |
| AggregateFlowFrames | 0.170 | 0.008 | 0.186 | |
| BuildMST | 2.462 | 0.071 | 2.668 | |
| BuildSOM | 2.541 | 0.101 | 2.789 | |
| CountGroups | 11.081 | 0.595 | 12.374 | |
| FMeasure | 0.003 | 0.001 | 0.004 | |
| FlowSOM | 26.086 | 1.012 | 29.497 | |
| FlowSOMSubset | 8.401 | 0.393 | 9.789 | |
| FlowSOMmary | 114.350 | 2.665 | 123.838 | |
| GetChannels | 0.069 | 0.005 | 0.074 | |
| GetClusterMFIs | 7.440 | 0.476 | 8.587 | |
| GetClusterPercentagesPositive | 7.485 | 0.480 | 8.319 | |
| GetClusters | 7.395 | 0.441 | 8.256 | |
| GetCounts | 7.472 | 0.496 | 8.364 | |
| GetFeatures | 11.880 | 0.384 | 13.063 | |
| GetFlowJoLabels | 15.755 | 0.625 | 17.292 | |
| GetMFIs | 8.030 | 0.662 | 9.612 | |
| GetMarkers | 0.070 | 0.005 | 0.085 | |
| GetMetaclusterCVs | 7.912 | 0.548 | 9.295 | |
| GetMetaclusterMFIs | 8.183 | 0.596 | 9.351 | |
| GetMetaclusterPercentagesPositive | 7.865 | 0.555 | 9.143 | |
| GetMetaclusters | 7.832 | 0.694 | 10.785 | |
| GetPercentages | 7.724 | 0.616 | 11.860 | |
| GroupStats | 33.275 | 1.057 | 40.704 | |
| Initialize_KWSP | 0.012 | 0.000 | 0.013 | |
| Initialize_PCA | 0.002 | 0.001 | 0.002 | |
| MetaClustering | 6.404 | 0.491 | 7.320 | |
| MetaclusterCVs | 8.012 | 0.588 | 9.357 | |
| MetaclusterMFIs | 9.054 | 0.699 | 10.282 | |
| NClusters | 9.450 | 0.741 | 10.704 | |
| NMetaclusters | 9.071 | 0.838 | 10.381 | |
| NewData | 7.342 | 0.484 | 8.354 | |
| Plot2DScatters | 22.072 | 0.739 | 23.606 | |
| PlotCenters | 2.362 | 0.068 | 2.542 | |
| PlotClusters2D | 2.377 | 0.117 | 2.628 | |
| PlotDimRed | 74.971 | 2.511 | 83.362 | |
| PlotFileScatters | 2.180 | 0.069 | 2.396 | |
| PlotFlowSOM | 12.128 | 0.681 | 13.851 | |
| PlotGroups | 28.177 | 0.954 | 31.749 | |
| PlotLabels | 10.597 | 0.606 | 11.877 | |
| PlotManualBars | 14.906 | 0.661 | 16.525 | |
| PlotMarker | 50.387 | 1.131 | 58.292 | |
| PlotNode | 15.975 | 0.690 | 17.976 | |
| PlotNumbers | 16.420 | 0.630 | 18.026 | |
| PlotOutliers | 36.231 | 0.792 | 39.936 | |
| PlotOverview2D | 7.959 | 0.560 | 9.040 | |
| PlotPies | 13.328 | 0.693 | 15.071 | |
| PlotSD | 5.373 | 0.190 | 6.100 | |
| PlotStars | 37.324 | 0.958 | 41.235 | |
| PlotVariable | 15.121 | 0.668 | 17.654 | |
| Purity | 0.001 | 0.001 | 0.002 | |
| QueryMultiple | 29.020 | 0.559 | 32.062 | |
| QueryStarPlot | 20.149 | 0.414 | 22.114 | |
| ReadInput | 6.607 | 0.488 | 7.928 | |
| SaveClustersToFCS | 9.630 | 0.725 | 11.608 | |
| TestOutliers | 8.614 | 0.532 | 10.045 | |
| UpdateMetaclusters | 45.108 | 1.185 | 50.959 | |
| UpdateNodeSize | 18.383 | 0.275 | 20.601 | |
| get_channels | 0.070 | 0.006 | 0.078 | |
| get_markers | 0.070 | 0.005 | 0.077 | |
| metaClustering_consensus | 5.310 | 0.360 | 5.848 | |
| plotStarLegend | 1.767 | 0.015 | 1.822 | |
| print.FlowSOM | 7.606 | 0.782 | 8.485 | |
| query_multiple | 28.803 | 0.485 | 29.911 | |