Back to Multiple platform build/check report for BioC 3.14
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-14 13:07:50 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 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 670/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.2.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_14
git_last_commit: 44e9c9b
git_last_commit_date: 2021-10-26 12:18:07 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 2.2.0
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_2.2.0.tar.gz
StartedAt: 2022-01-13 13:06:48 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 13:20:43 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 834.8 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.2.0’
* 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 ... 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        89.830  2.535  92.527
PlotDimRed         71.307  1.498  72.882
UpdateMetaclusters 34.805  1.637  36.491
PlotMarker         30.472  1.622  32.134
GroupStats         24.640  1.515  26.191
PlotGroups         22.694  1.856  24.581
FlowSOM            22.233  1.639  23.957
AddAnnotation      15.760  0.907  16.743
UpdateNodeSize     14.522  0.514  15.059
query_multiple     14.681  0.349  15.068
QueryMultiple      14.493  0.352  14.861
PlotNode           12.243  1.070  13.333
PlotStars          11.778  0.831  12.625
QueryStarPlot      11.960  0.308  12.315
PlotPies           11.089  0.871  11.971
Plot2DScatters     10.670  0.945  11.766
PlotManualBars     10.083  1.474  11.573
PlotFlowSOM        10.481  1.060  11.559
GetFlowJoLabels    10.036  0.752  10.807
PlotNumbers         9.754  0.883  10.653
CountGroups         8.362  0.988   9.365
TestOutliers        7.266  1.109   8.381
NMetaclusters       6.892  1.216   8.125
PlotVariable        7.269  0.779   8.057
NClusters           6.719  1.312   8.051
SaveClustersToFCS   6.945  0.962   7.957
MetaclusterMFIs     6.945  0.937   7.901
PlotLabels          6.748  1.068   7.889
GetFeatures         7.096  0.533   7.636
GetMetaclusters     5.820  1.137   6.967
print.FlowSOM       6.104  0.846   6.958
GetMetaclusterMFIs  5.795  1.130   6.936
FlowSOMSubset       6.354  0.547   6.912
GetMetaclusterCVs   6.005  0.775   6.792
GetPercentages      5.908  0.832   6.755
PlotOverview2D      5.521  1.077   6.604
MetaclusterCVs      5.843  0.735   6.591
GetMFIs             5.634  0.913   6.561
GetClusters         5.968  0.533   6.508
GetCounts           5.963  0.502   6.483
GetClusterMFIs      5.822  0.503   6.417
ReadInput           5.200  0.719   5.927
NewData             5.060  0.435   5.508
MetaClustering      4.722  0.403   5.212
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
AddAnnotation15.760 0.90716.743
AggregateFlowFrames0.1470.0040.151
BuildMST1.7520.1041.858
BuildSOM1.8350.0811.922
CountGroups8.3620.9889.365
FMeasure0.0030.0010.003
FlowSOM22.233 1.63923.957
FlowSOMSubset6.3540.5476.912
FlowSOMmary89.830 2.53592.527
GetChannels0.0480.0020.051
GetClusterMFIs5.8220.5036.417
GetClusters5.9680.5336.508
GetCounts5.9630.5026.483
GetFeatures7.0960.5337.636
GetFlowJoLabels10.036 0.75210.807
GetMFIs5.6340.9136.561
GetMarkers0.0640.0030.066
GetMetaclusterCVs6.0050.7756.792
GetMetaclusterMFIs5.7951.1306.936
GetMetaclusters5.8201.1376.967
GetPercentages5.9080.8326.755
GroupStats24.640 1.51526.191
Initialize_KWSP0.0100.0000.011
Initialize_PCA0.0000.0000.001
MetaClustering4.7220.4035.212
MetaclusterCVs5.8430.7356.591
MetaclusterMFIs6.9450.9377.901
NClusters6.7191.3128.051
NMetaclusters6.8921.2168.125
NewData5.0600.4355.508
Plot2DScatters10.670 0.94511.766
PlotCenters1.7090.1141.825
PlotClusters2D1.6440.1091.754
PlotDimRed71.307 1.49872.882
PlotFileScatters1.1440.0121.156
PlotFlowSOM10.481 1.06011.559
PlotGroups22.694 1.85624.581
PlotLabels6.7481.0687.889
PlotManualBars10.083 1.47411.573
PlotMarker30.472 1.62232.134
PlotNode12.243 1.07013.333
PlotNumbers 9.754 0.88310.653
PlotOverview2D5.5211.0776.604
PlotPies11.089 0.87111.971
PlotSD3.6570.1373.798
PlotStars11.778 0.83112.625
PlotVariable7.2690.7798.057
Purity0.0010.0000.001
QueryMultiple14.493 0.35214.861
QueryStarPlot11.960 0.30812.315
ReadInput5.2000.7195.927
SaveClustersToFCS6.9450.9627.957
TestOutliers7.2661.1098.381
UpdateMetaclusters34.805 1.63736.491
UpdateNodeSize14.522 0.51415.059
get_channels0.0580.0020.061
get_markers0.0770.0100.087
metaClustering_consensus4.0510.3744.430
plotStarLegend0.5040.0040.508
print.FlowSOM6.1040.8466.958
query_multiple14.681 0.34915.068