Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-05 11:43 -0400 (Sat, 05 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 737/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.13.0 (landing page) Sofie Van Gassen
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 2024-10-04 21:17:20 -0400 (Fri, 04 Oct 2024) |
EndedAt: 2024-10-04 21:20:30 -0400 (Fri, 04 Oct 2024) |
EllapsedTime: 190.2 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 (2024-06-14) * 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 13.6.7 * 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 17.858 1.029 18.804 PlotDimRed 16.453 1.381 17.931 PlotMarker 5.731 0.467 6.235 PlotOutliers 5.239 0.412 5.671 UpdateMetaclusters 5.007 0.341 5.360 PlotStars 4.624 0.370 5.015 * 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 | 2.941 | 0.187 | 3.139 | |
AggregateFlowFrames | 0.029 | 0.003 | 0.031 | |
BuildMST | 0.531 | 0.050 | 0.582 | |
BuildSOM | 0.372 | 0.042 | 0.413 | |
CountGroups | 2.097 | 0.222 | 2.324 | |
FMeasure | 0.000 | 0.000 | 0.001 | |
FlowSOM | 4.082 | 0.275 | 4.408 | |
FlowSOMSubset | 1.386 | 0.093 | 1.513 | |
FlowSOMmary | 17.858 | 1.029 | 18.804 | |
GetChannels | 0.012 | 0.001 | 0.014 | |
GetClusterMFIs | 1.476 | 0.207 | 1.685 | |
GetClusterPercentagesPositive | 1.475 | 0.205 | 1.696 | |
GetClusters | 1.474 | 0.254 | 1.730 | |
GetCounts | 1.539 | 0.330 | 1.879 | |
GetFeatures | 1.808 | 0.235 | 2.404 | |
GetFlowJoLabels | 2.639 | 0.398 | 3.158 | |
GetMFIs | 1.617 | 0.266 | 1.957 | |
GetMarkers | 0.012 | 0.001 | 0.013 | |
GetMetaclusterCVs | 1.503 | 0.239 | 1.741 | |
GetMetaclusterMFIs | 1.707 | 0.246 | 1.966 | |
GetMetaclusterPercentagesPositive | 1.768 | 0.244 | 2.026 | |
GetMetaclusters | 1.618 | 0.251 | 1.898 | |
GetPercentages | 1.773 | 0.235 | 2.017 | |
GroupStats | 4.106 | 0.480 | 4.592 | |
Initialize_KWSP | 0.001 | 0.000 | 0.002 | |
Initialize_PCA | 0 | 0 | 0 | |
MetaClustering | 1.041 | 0.211 | 1.256 | |
MetaclusterCVs | 1.540 | 0.251 | 1.805 | |
MetaclusterMFIs | 1.759 | 0.267 | 2.029 | |
NClusters | 1.671 | 0.264 | 1.936 | |
NMetaclusters | 1.799 | 0.284 | 2.082 | |
NewData | 1.305 | 0.175 | 1.479 | |
Plot2DScatters | 2.525 | 0.259 | 2.798 | |
PlotCenters | 0.399 | 0.049 | 0.448 | |
PlotClusters2D | 0.394 | 0.036 | 0.430 | |
PlotDimRed | 16.453 | 1.381 | 17.931 | |
PlotFileScatters | 0.235 | 0.011 | 0.256 | |
PlotFlowSOM | 1.995 | 0.303 | 2.348 | |
PlotGroups | 3.612 | 0.581 | 4.244 | |
PlotLabels | 1.935 | 0.235 | 2.172 | |
PlotManualBars | 2.455 | 0.255 | 2.712 | |
PlotMarker | 5.731 | 0.467 | 6.235 | |
PlotNode | 2.343 | 0.314 | 2.695 | |
PlotNumbers | 2.298 | 0.296 | 2.596 | |
PlotOutliers | 5.239 | 0.412 | 5.671 | |
PlotOverview2D | 1.757 | 0.274 | 2.033 | |
PlotPies | 2.269 | 0.279 | 2.553 | |
PlotSD | 0.712 | 0.072 | 0.784 | |
PlotStars | 4.624 | 0.370 | 5.015 | |
PlotVariable | 2.328 | 0.277 | 2.621 | |
Purity | 0 | 0 | 0 | |
QueryMultiple | 2.853 | 0.284 | 3.151 | |
QueryStarPlot | 2.077 | 0.139 | 2.216 | |
ReadInput | 0.969 | 0.199 | 1.169 | |
SaveClustersToFCS | 1.805 | 0.288 | 2.105 | |
TestOutliers | 1.734 | 0.241 | 1.994 | |
UpdateMetaclusters | 5.007 | 0.341 | 5.360 | |
UpdateNodeSize | 1.761 | 0.100 | 1.865 | |
get_channels | 0.013 | 0.002 | 0.014 | |
get_markers | 0.012 | 0.001 | 0.013 | |
metaClustering_consensus | 1.007 | 0.199 | 1.217 | |
plotStarLegend | 0.138 | 0.001 | 0.140 | |
print.FlowSOM | 1.583 | 0.341 | 1.953 | |
query_multiple | 2.833 | 0.174 | 3.021 | |