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CHECK report for FlowSOM on merida1

This page was generated on 2021-05-06 12:35:00 -0400 (Thu, 06 May 2021).

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 631/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.22.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: RELEASE_3_12
Last Commit: 89cd5ba
Last Changed Date: 2020-10-27 11:01:34 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: FlowSOM
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2021-05-06 01:50:24 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:54:32 -0400 (Thu, 06 May 2021)
EllapsedTime: 248.2 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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.22.0’
* 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-3.12-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     11.659  0.891  12.576
FlowSOM          8.789  0.661   9.473
PlotOverview2D   7.632  0.342   8.039
MetaclusterMFIs  5.495  0.424   5.936
TestOutliers     5.291  0.407   5.753
ReadInput        5.024  0.366   5.406
FlowSOMSubset    4.958  0.382   5.351
PlotPies         4.774  0.298   5.084
GetFlowJoLabels  4.663  0.343   5.025
GetMFIs          4.656  0.337   5.003
* 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-3.12-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
AggregateFlowFrames0.1900.0130.203
BuildMST1.6410.0881.733
BuildSOM1.6710.0761.751
CountGroups11.659 0.89112.576
FMeasure0.0020.0010.002
FlowSOM8.7890.6619.473
FlowSOMSubset4.9580.3825.351
GetClusters4.4800.2614.755
GetFlowJoLabels4.6630.3435.025
GetMFIs4.6560.3375.003
GetMetaclusters4.2940.2954.600
Initialize_KWSP0.0080.0000.008
Initialize_PCA0.0030.0000.003
MetaClustering4.4830.2704.769
MetaclusterCVs4.1120.2914.454
MetaclusterMFIs5.4950.4245.936
NewData3.9970.2654.271
PlotCenters1.4320.0691.504
PlotClusters2D1.3840.0701.456
PlotGroups0.0000.0000.001
PlotLabels4.1400.2894.473
PlotMarker1.6030.0891.695
PlotNode4.0190.3414.373
PlotNumbers1.3060.0501.357
PlotOverview2D7.6320.3428.039
PlotPies4.7740.2985.084
PlotSD1.4530.0421.497
PlotStars1.2570.0591.318
PlotVariable1.4430.0491.494
Purity0.0020.0010.002
QueryStarPlot2.9440.1193.071
ReadInput5.0240.3665.406
TestOutliers5.2910.4075.753
UpdateNodeSize1.5580.0721.634
get_channels0.0550.0010.058
get_markers0.0580.0020.060
metaClustering_consensus3.4520.3223.890