Back to Multiple platform build/check report for BioC 3.13
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:36 -0400 (Fri, 15 Oct 2021).

CHECK results for FlowSOM on machv2

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? here 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 661/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.0.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_13
git_last_commit: 663dedc
git_last_commit_date: 2021-05-19 12:10:09 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FlowSOM
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowSOM_2.0.0.tar.gz
StartedAt: 2021-10-14 19:08:38 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 19:20:47 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 728.8 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowSOM_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... 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          76.913  2.009  79.106
PlotDimRed           60.054  1.599  61.743
RelabelMetaclusters  30.179  1.453  31.662
PlotMarker           25.869  1.297  27.226
GroupStats           21.569  1.326  22.931
ReassignMetaclusters 20.625  1.109  21.763
PlotGroups           18.924  1.331  20.400
FlowSOM              17.715  1.262  19.008
AddAnnotation        13.011  0.712  13.792
QueryMultiple        13.238  0.383  13.636
query_multiple       12.579  0.320  12.929
UpdateNodeSize       11.989  0.474  12.475
PlotNode             10.505  1.204  11.724
PlotStars            10.045  0.887  10.948
QueryStarPlot         9.917  0.464  10.393
Plot2DScatters        9.332  0.698  10.058
PlotManualBars        8.561  0.672   9.261
PlotNumbers           8.291  0.831   9.135
PlotPies              8.342  0.694   9.144
GetFlowJoLabels       8.344  0.469   8.860
PlotFlowSOM           7.876  0.852   8.744
CountGroups           7.224  0.752   7.986
PlotVariable          6.001  0.691   6.700
NMetaclusters         5.790  0.887   6.689
PlotLabels            5.981  0.626   6.616
SaveClustersToFCS     5.729  0.727   6.467
print.FlowSOM         5.435  0.905   6.350
TestOutliers          5.625  0.647   6.359
GetFeatures           6.046  0.211   6.269
NClusters             5.502  0.696   6.215
MetaclusterMFIs       5.267  0.724   6.012
GetClusterMFIs        5.393  0.392   5.793
GetCounts             5.190  0.521   5.732
GetMetaclusterMFIs    5.014  0.601   5.628
GetMFIs               4.743  0.838   5.593
MetaclusterCVs        4.807  0.757   5.587
GetMetaclusters       4.970  0.512   5.492
FlowSOMSubset         5.146  0.323   5.485
GetClusters           4.798  0.493   5.296
GetMetaclusterCVs     4.462  0.686   5.156
ReadInput             4.500  0.574   5.090
GetPercentages        4.457  0.592   5.065
* 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-3.13-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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
AddAnnotation13.011 0.71213.792
AggregateFlowFrames0.1200.0030.124
BuildMST1.5670.0981.666
BuildSOM2.0810.0872.169
CountGroups7.2240.7527.986
FMeasure0.0010.0000.002
FlowSOM17.715 1.26219.008
FlowSOMSubset5.1460.3235.485
FlowSOMmary76.913 2.00979.106
GetChannels0.0590.0020.061
GetClusterMFIs5.3930.3925.793
GetClusters4.7980.4935.296
GetCounts5.1900.5215.732
GetFeatures6.0460.2116.269
GetFlowJoLabels8.3440.4698.860
GetMFIs4.7430.8385.593
GetMarkers0.0520.0020.054
GetMetaclusterCVs4.4620.6865.156
GetMetaclusterMFIs5.0140.6015.628
GetMetaclusters4.9700.5125.492
GetPercentages4.4570.5925.065
GroupStats21.569 1.32622.931
Initialize_KWSP0.0080.0000.008
Initialize_PCA0.0010.0010.001
MetaClustering4.2370.6214.924
MetaclusterCVs4.8070.7575.587
MetaclusterMFIs5.2670.7246.012
NClusters5.5020.6966.215
NMetaclusters5.7900.8876.689
NewData4.3920.3584.805
Plot2DScatters 9.332 0.69810.058
PlotCenters1.5660.0851.654
PlotClusters2D1.5930.1351.730
PlotDimRed60.054 1.59961.743
PlotFileScatters0.8110.0220.835
PlotFlowSOM7.8760.8528.744
PlotGroups18.924 1.33120.400
PlotLabels5.9810.6266.616
PlotManualBars8.5610.6729.261
PlotMarker25.869 1.29727.226
PlotNode10.505 1.20411.724
PlotNumbers8.2910.8319.135
PlotOverview2D4.4310.5264.962
PlotPies8.3420.6949.144
PlotSD2.6830.2232.911
PlotStars10.045 0.88710.948
PlotVariable6.0010.6916.700
Purity0.0010.0010.001
QueryMultiple13.238 0.38313.636
QueryStarPlot 9.917 0.46410.393
ReadInput4.5000.5745.090
ReassignMetaclusters20.625 1.10921.763
RelabelMetaclusters30.179 1.45331.662
SaveClustersToFCS5.7290.7276.467
TestOutliers5.6250.6476.359
UpdateNodeSize11.989 0.47412.475
get_channels0.0550.0020.057
get_markers0.0510.0020.054
metaClustering_consensus3.4200.3673.793
plotStarLegend0.4880.0030.493
print.FlowSOM5.4350.9056.350
query_multiple12.579 0.32012.929