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CHECK report for FlowSOM on machv2

This page was generated on 2020-10-17 11:58:29 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE FlowSOM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 623/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.20.0
Sofie Van Gassen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: RELEASE_3_11
Last Commit: 13887e0
Last Changed Date: 2020-04-27 14:45:50 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FlowSOM
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2020-10-17 01:13:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:18:06 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 256.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FlowSOM.Rcheck
Warnings: 1

Command output

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### 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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/FlowSOM.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.20.0’
* 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 ... WARNING
Found the following significant warnings:
  som.c:37:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  som.c:47:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  som.c:134:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/FlowSOM.Rcheck/00install.out’ for details.
* 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
AddFlowFrame: no visible global function definition for ‘is’
ReadInput: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
CountGroups     13.700  1.069  14.871
FlowSOM         10.145  0.880  11.042
PlotOverview2D   6.232  0.613   7.078
TestOutliers     5.622  0.547   6.200
MetaclusterMFIs  5.420  0.659   6.122
PlotPies         5.225  0.579   5.831
ReadInput        5.213  0.589   5.815
FlowSOMSubset    5.234  0.480   5.727
GetFlowJoLabels  5.096  0.376   5.491
PlotNode         4.921  0.511   5.444
MetaClustering   4.812  0.409   5.232
MetaclusterCVs   4.641  0.542   5.191
GetMetaclusters  4.756  0.409   5.173
GetClusters      4.487  0.539   5.040
GetMFIs          4.624  0.401   5.072
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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
som.c:37:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        xdist += abs(tmp);
                 ^
som.c:37:18: note: use function 'fabs' instead
        xdist += abs(tmp);
                 ^~~
                 fabs
som.c:47:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        tmp = abs(tmp);
              ^
som.c:47:15: note: use function 'fabs' instead
        tmp = abs(tmp);
              ^~~
              fabs
som.c:134:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
                change += abs(tmp);
                          ^
som.c:134:27: note: use function 'fabs' instead
                change += abs(tmp);
                          ^~~
                          fabs
3 warnings generated.
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/4.0/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
AggregateFlowFrames0.2260.0230.249
BuildMST1.6560.1261.784
BuildSOM2.3860.1362.552
CountGroups13.700 1.06914.871
FMeasure0.0040.0010.004
FlowSOM10.145 0.88011.042
FlowSOMSubset5.2340.4805.727
GetClusters4.4870.5395.040
GetFlowJoLabels5.0960.3765.491
GetMFIs4.6240.4015.072
GetMetaclusters4.7560.4095.173
Initialize_KWSP0.0050.0000.006
Initialize_PCA0.0010.0000.002
MetaClustering4.8120.4095.232
MetaclusterCVs4.6410.5425.191
MetaclusterMFIs5.4200.6596.122
NewData4.2230.4364.669
PlotCenters1.8130.0851.901
PlotClusters2D1.5950.0991.695
PlotGroups0.0000.0000.001
PlotLabels4.4910.3934.894
PlotMarker1.5750.0841.661
PlotNode4.9210.5115.444
PlotNumbers1.6950.0511.748
PlotOverview2D6.2320.6137.078
PlotPies5.2250.5795.831
PlotSD1.8340.0711.907
PlotStars1.8800.1161.999
PlotVariable1.6920.0801.774
Purity0.0010.0010.002
QueryStarPlot3.3700.1403.515
ReadInput5.2130.5895.815
TestOutliers5.6220.5476.200
UpdateNodeSize1.8470.0821.931
get_channels0.0610.0030.064
get_markers0.0660.0030.070
metaClustering_consensus3.6670.2533.930