Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:39:16 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 743/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.11.0 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | 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: 2.11.0 |
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_2.11.0.tar.gz |
StartedAt: 2024-03-27 21:12:28 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 21:24:21 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 713.2 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_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.11.0’ * 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 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 68.290 2.756 71.570 PlotDimRed 44.063 2.863 47.626 PlotMarker 29.531 1.536 31.545 UpdateMetaclusters 26.345 1.666 28.388 PlotStars 21.310 1.350 22.977 PlotOutliers 20.517 1.041 21.846 GroupStats 20.021 1.205 21.553 query_multiple 17.424 0.661 18.249 QueryMultiple 17.302 0.644 18.202 PlotGroups 16.377 1.352 18.046 FlowSOM 14.702 1.208 16.107 Plot2DScatters 13.058 0.981 14.281 AddAnnotation 13.208 0.785 14.139 QueryStarPlot 12.168 0.456 12.835 PlotNumbers 9.811 1.115 11.105 UpdateNodeSize 10.387 0.381 10.863 GetFlowJoLabels 9.735 0.747 10.589 PlotNode 9.449 0.952 10.547 PlotVariable 9.345 0.987 10.506 PlotPies 8.745 0.892 9.832 PlotManualBars 8.611 1.012 9.779 PlotFlowSOM 7.721 0.878 8.736 PlotLabels 6.547 0.828 7.519 SaveClustersToFCS 6.300 1.003 7.407 CountGroups 6.559 0.647 7.303 GetFeatures 6.151 0.500 6.723 NClusters 5.616 1.020 6.719 MetaclusterMFIs 5.539 0.881 6.505 NMetaclusters 5.321 0.937 6.332 TestOutliers 5.357 0.792 6.251 GetPercentages 5.295 0.765 6.170 GetMFIs 5.273 0.753 6.110 MetaclusterCVs 5.184 0.745 6.041 GetMetaclusters 4.976 0.841 5.937 PlotOverview2D 5.058 0.759 5.910 GetMetaclusterPercentagesPositive 4.988 0.708 5.742 GetMetaclusterMFIs 4.876 0.750 5.686 print.FlowSOM 4.895 0.704 5.656 GetMetaclusterCVs 4.753 0.731 5.564 GetClusters 4.627 0.629 5.316 GetCounts 4.710 0.530 5.316 NewData 4.659 0.580 5.334 GetClusterMFIs 4.579 0.539 5.185 FlowSOMSubset 4.629 0.479 5.168 GetClusterPercentagesPositive 4.521 0.506 5.084 * 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-3.19-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-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/4.4-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 | 13.208 | 0.785 | 14.139 | |
AggregateFlowFrames | 0.110 | 0.007 | 0.117 | |
BuildMST | 1.472 | 0.107 | 1.599 | |
BuildSOM | 1.591 | 0.110 | 1.726 | |
CountGroups | 6.559 | 0.647 | 7.303 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 14.702 | 1.208 | 16.107 | |
FlowSOMSubset | 4.629 | 0.479 | 5.168 | |
FlowSOMmary | 68.290 | 2.756 | 71.570 | |
GetChannels | 0.044 | 0.003 | 0.048 | |
GetClusterMFIs | 4.579 | 0.539 | 5.185 | |
GetClusterPercentagesPositive | 4.521 | 0.506 | 5.084 | |
GetClusters | 4.627 | 0.629 | 5.316 | |
GetCounts | 4.710 | 0.530 | 5.316 | |
GetFeatures | 6.151 | 0.500 | 6.723 | |
GetFlowJoLabels | 9.735 | 0.747 | 10.589 | |
GetMFIs | 5.273 | 0.753 | 6.110 | |
GetMarkers | 0.048 | 0.003 | 0.051 | |
GetMetaclusterCVs | 4.753 | 0.731 | 5.564 | |
GetMetaclusterMFIs | 4.876 | 0.750 | 5.686 | |
GetMetaclusterPercentagesPositive | 4.988 | 0.708 | 5.742 | |
GetMetaclusters | 4.976 | 0.841 | 5.937 | |
GetPercentages | 5.295 | 0.765 | 6.170 | |
GroupStats | 20.021 | 1.205 | 21.553 | |
Initialize_KWSP | 0.005 | 0.001 | 0.006 | |
Initialize_PCA | 0.001 | 0.001 | 0.001 | |
MetaClustering | 3.844 | 0.713 | 4.671 | |
MetaclusterCVs | 5.184 | 0.745 | 6.041 | |
MetaclusterMFIs | 5.539 | 0.881 | 6.505 | |
NClusters | 5.616 | 1.020 | 6.719 | |
NMetaclusters | 5.321 | 0.937 | 6.332 | |
NewData | 4.659 | 0.580 | 5.334 | |
Plot2DScatters | 13.058 | 0.981 | 14.281 | |
PlotCenters | 1.314 | 0.088 | 1.426 | |
PlotClusters2D | 1.295 | 0.119 | 1.435 | |
PlotDimRed | 44.063 | 2.863 | 47.626 | |
PlotFileScatters | 1.293 | 0.080 | 1.392 | |
PlotFlowSOM | 7.721 | 0.878 | 8.736 | |
PlotGroups | 16.377 | 1.352 | 18.046 | |
PlotLabels | 6.547 | 0.828 | 7.519 | |
PlotManualBars | 8.611 | 1.012 | 9.779 | |
PlotMarker | 29.531 | 1.536 | 31.545 | |
PlotNode | 9.449 | 0.952 | 10.547 | |
PlotNumbers | 9.811 | 1.115 | 11.105 | |
PlotOutliers | 20.517 | 1.041 | 21.846 | |
PlotOverview2D | 5.058 | 0.759 | 5.910 | |
PlotPies | 8.745 | 0.892 | 9.832 | |
PlotSD | 3.058 | 0.251 | 3.351 | |
PlotStars | 21.310 | 1.350 | 22.977 | |
PlotVariable | 9.345 | 0.987 | 10.506 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 17.302 | 0.644 | 18.202 | |
QueryStarPlot | 12.168 | 0.456 | 12.835 | |
ReadInput | 3.797 | 0.716 | 4.619 | |
SaveClustersToFCS | 6.300 | 1.003 | 7.407 | |
TestOutliers | 5.357 | 0.792 | 6.251 | |
UpdateMetaclusters | 26.345 | 1.666 | 28.388 | |
UpdateNodeSize | 10.387 | 0.381 | 10.863 | |
get_channels | 0.043 | 0.003 | 0.046 | |
get_markers | 0.043 | 0.003 | 0.047 | |
metaClustering_consensus | 2.815 | 0.631 | 3.487 | |
plotStarLegend | 1.025 | 0.024 | 1.060 | |
print.FlowSOM | 4.895 | 0.704 | 5.656 | |
query_multiple | 17.424 | 0.661 | 18.249 | |