Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:07:40 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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

CHECK results for FlowSOM on merida1


To the developers/maintainers of the FlowSOM package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 691/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.4.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_15
git_last_commit: bf61833
git_last_commit_date: 2022-04-26 11:23:11 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FlowSOM
Version: 2.4.0
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_2.4.0.tar.gz
StartedAt: 2022-05-16 02:26:32 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 02:43:28 -0400 (Mon, 16 May 2022)
EllapsedTime: 1016.6 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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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_2.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/FlowSOM.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.4.0’
* 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
* 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 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 ... NOTE
Plot2DScatters: no visible binding for global variable ‘Population’
Undefined global functions or variables:
  Population
* 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                       104.246  2.619 107.179
PlotDimRed                         80.913  1.754  86.081
UpdateMetaclusters                 40.678  1.560  42.327
PlotMarker                         35.941  1.366  38.157
GroupStats                         32.746  1.194  34.972
PlotGroups                         28.458  1.236  29.802
FlowSOM                            25.595  1.569  27.309
AddAnnotation                      18.930  1.069  20.322
UpdateNodeSize                     16.896  0.454  17.373
QueryMultiple                      16.762  0.399  17.199
query_multiple                     16.292  0.420  16.762
PlotNode                           14.961  0.631  16.386
PlotStars                          14.397  0.820  15.249
Plot2DScatters                     13.797  1.087  14.929
PlotManualBars                     13.747  0.929  15.119
QueryStarPlot                      13.389  0.281  13.704
PlotFlowSOM                        12.668  0.879  13.580
PlotPies                           12.414  0.967  13.520
GetFlowJoLabels                    12.447  0.649  13.153
PlotNumbers                        11.874  0.830  12.736
GetFeatures                        11.681  0.373  12.080
CountGroups                        11.146  0.871  12.162
PlotVariable                        9.428  0.737  10.202
PlotLabels                          9.361  0.610  11.056
SaveClustersToFCS                   9.055  0.898   9.985
TestOutliers                        9.004  0.878   9.911
NClusters                           8.446  1.034   9.502
NMetaclusters                       8.518  0.931   9.493
FlowSOMSubset                       8.691  0.520   9.254
MetaclusterMFIs                     8.388  0.713   9.118
MetaclusterCVs                      8.022  0.703   9.126
GetPercentages                      7.922  0.678   8.617
GetMFIs                             7.545  0.938   8.505
GetMetaclusterMFIs                  7.520  0.692   8.235
GetMetaclusters                     7.491  0.704   8.208
PlotOverview2D                      7.343  0.746   8.105
GetClusterMFIs                      7.512  0.561   8.094
GetMetaclusterPercentagesPositive   7.468  0.590   8.084
GetMetaclusterCVs                   7.388  0.648   8.062
GetClusterPercentagesPositive       7.473  0.537   8.029
GetCounts                           7.486  0.468   7.974
GetClusters                         7.473  0.468   7.968
print.FlowSOM                       7.049  0.707   7.770
NewData                             6.971  0.507   7.503
ReadInput                           6.156  0.537   6.714
MetaClustering                      6.156  0.428   6.646
metaClustering_consensus            5.174  0.791   5.976
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c som.c -o som.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/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)

Tests output


Example timings

FlowSOM.Rcheck/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation18.930 1.06920.322
AggregateFlowFrames0.1800.0060.185
BuildMST2.7000.0712.901
BuildSOM2.7390.0972.928
CountGroups11.146 0.87112.162
FMeasure0.0030.0000.003
FlowSOM25.595 1.56927.309
FlowSOMSubset8.6910.5209.254
FlowSOMmary104.246 2.619107.179
GetChannels0.0620.0020.065
GetClusterMFIs7.5120.5618.094
GetClusterPercentagesPositive7.4730.5378.029
GetClusters7.4730.4687.968
GetCounts7.4860.4687.974
GetFeatures11.681 0.37312.080
GetFlowJoLabels12.447 0.64913.153
GetMFIs7.5450.9388.505
GetMarkers0.0660.0020.068
GetMetaclusterCVs7.3880.6488.062
GetMetaclusterMFIs7.5200.6928.235
GetMetaclusterPercentagesPositive7.4680.5908.084
GetMetaclusters7.4910.7048.208
GetPercentages7.9220.6788.617
GroupStats32.746 1.19434.972
Initialize_KWSP0.010.000.01
Initialize_PCA0.0010.0010.002
MetaClustering6.1560.4286.646
MetaclusterCVs8.0220.7039.126
MetaclusterMFIs8.3880.7139.118
NClusters8.4461.0349.502
NMetaclusters8.5180.9319.493
NewData6.9710.5077.503
Plot2DScatters13.797 1.08714.929
PlotCenters2.3220.1772.500
PlotClusters2D2.2950.3132.611
PlotDimRed80.913 1.75486.081
PlotFileScatters1.7020.0621.768
PlotFlowSOM12.668 0.87913.580
PlotGroups28.458 1.23629.802
PlotLabels 9.361 0.61011.056
PlotManualBars13.747 0.92915.119
PlotMarker35.941 1.36638.157
PlotNode14.961 0.63116.386
PlotNumbers11.874 0.83012.736
PlotOverview2D7.3430.7468.105
PlotPies12.414 0.96713.520
PlotSD4.2710.1624.446
PlotStars14.397 0.82015.249
PlotVariable 9.428 0.73710.202
Purity0.0010.0010.001
QueryMultiple16.762 0.39917.199
QueryStarPlot13.389 0.28113.704
ReadInput6.1560.5376.714
SaveClustersToFCS9.0550.8989.985
TestOutliers9.0040.8789.911
UpdateMetaclusters40.678 1.56042.327
UpdateNodeSize16.896 0.45417.373
get_channels0.0660.0020.069
get_markers0.0630.0020.064
metaClustering_consensus5.1740.7915.976
plotStarLegend0.5590.0060.566
print.FlowSOM7.0490.7077.770
query_multiple16.292 0.42016.762