Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-25 11:39 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 727/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.13.0 (landing page) Sofie Van Gassen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: 2.13.0 |
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_2.13.0.tar.gz |
StartedAt: 2024-06-24 20:49:09 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 20:52:20 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 191.2 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_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: aarch64-apple-darwin20 * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.13.0’ * 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-1500.1.0.2.5)’ * 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 code 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 whether 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 ... NOTE checkRd: (-1) PlotDimRed.Rd:55: Lost braces 55 | of the dimred default = function(dimred){dimred$Y}.} | ^ * 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 17.820 0.827 18.539 PlotDimRed 16.580 1.410 18.019 PlotMarker 6.047 0.491 6.544 UpdateMetaclusters 5.539 0.493 6.043 PlotOutliers 5.450 0.359 5.816 PlotStars 4.742 0.348 5.090 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-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/4.4-arm64/Resources/library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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/4.4-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 | 2.805 | 0.149 | 2.956 | |
AggregateFlowFrames | 0.026 | 0.002 | 0.028 | |
BuildMST | 0.396 | 0.007 | 0.404 | |
BuildSOM | 0.349 | 0.016 | 0.365 | |
CountGroups | 1.953 | 0.109 | 2.063 | |
FMeasure | 0.001 | 0.000 | 0.000 | |
FlowSOM | 3.997 | 0.226 | 4.228 | |
FlowSOMSubset | 1.651 | 0.094 | 1.751 | |
FlowSOMmary | 17.820 | 0.827 | 18.539 | |
GetChannels | 0.013 | 0.002 | 0.015 | |
GetClusterMFIs | 1.514 | 0.188 | 1.706 | |
GetClusterPercentagesPositive | 1.573 | 0.268 | 1.842 | |
GetClusters | 1.540 | 0.276 | 1.816 | |
GetCounts | 1.393 | 0.233 | 1.626 | |
GetFeatures | 1.810 | 0.177 | 1.993 | |
GetFlowJoLabels | 2.565 | 0.280 | 2.848 | |
GetMFIs | 1.564 | 0.199 | 1.763 | |
GetMarkers | 0.013 | 0.001 | 0.014 | |
GetMetaclusterCVs | 1.611 | 0.228 | 1.840 | |
GetMetaclusterMFIs | 1.513 | 0.172 | 1.685 | |
GetMetaclusterPercentagesPositive | 1.582 | 0.266 | 1.849 | |
GetMetaclusters | 1.659 | 0.264 | 1.930 | |
GetPercentages | 1.704 | 0.294 | 1.999 | |
GroupStats | 4.044 | 0.352 | 4.398 | |
Initialize_KWSP | 0.001 | 0.000 | 0.002 | |
Initialize_PCA | 0.001 | 0.000 | 0.000 | |
MetaClustering | 1.041 | 0.204 | 1.245 | |
MetaclusterCVs | 1.535 | 0.224 | 1.759 | |
MetaclusterMFIs | 1.780 | 0.272 | 2.054 | |
NClusters | 1.834 | 0.320 | 2.155 | |
NMetaclusters | 1.758 | 0.262 | 2.022 | |
NewData | 1.332 | 0.148 | 1.482 | |
Plot2DScatters | 2.764 | 0.377 | 3.143 | |
PlotCenters | 0.614 | 0.057 | 0.672 | |
PlotClusters2D | 0.401 | 0.060 | 0.461 | |
PlotDimRed | 16.580 | 1.410 | 18.019 | |
PlotFileScatters | 0.245 | 0.010 | 0.255 | |
PlotFlowSOM | 2.056 | 0.326 | 2.382 | |
PlotGroups | 3.583 | 0.407 | 3.993 | |
PlotLabels | 1.879 | 0.252 | 2.137 | |
PlotManualBars | 2.549 | 0.319 | 2.870 | |
PlotMarker | 6.047 | 0.491 | 6.544 | |
PlotNode | 2.339 | 0.242 | 2.582 | |
PlotNumbers | 2.296 | 0.330 | 2.629 | |
PlotOutliers | 5.450 | 0.359 | 5.816 | |
PlotOverview2D | 1.823 | 0.232 | 2.057 | |
PlotPies | 2.360 | 0.326 | 2.687 | |
PlotSD | 0.749 | 0.064 | 0.813 | |
PlotStars | 4.742 | 0.348 | 5.090 | |
PlotVariable | 2.294 | 0.290 | 2.585 | |
Purity | 0.001 | 0.000 | 0.000 | |
QueryMultiple | 3.115 | 0.180 | 3.303 | |
QueryStarPlot | 2.381 | 0.140 | 2.522 | |
ReadInput | 1.078 | 0.220 | 1.303 | |
SaveClustersToFCS | 1.990 | 0.322 | 2.324 | |
TestOutliers | 1.815 | 0.232 | 2.052 | |
UpdateMetaclusters | 5.539 | 0.493 | 6.043 | |
UpdateNodeSize | 1.747 | 0.094 | 1.842 | |
get_channels | 0.013 | 0.001 | 0.014 | |
get_markers | 0.013 | 0.001 | 0.014 | |
metaClustering_consensus | 0.873 | 0.146 | 1.019 | |
plotStarLegend | 0.149 | 0.001 | 0.151 | |
print.FlowSOM | 1.654 | 0.228 | 1.887 | |
query_multiple | 3.063 | 0.137 | 3.202 | |