BioC 3.6: CHECK report for FlowSOM on veracruz1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FlowSOM_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/FlowSOM.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘1.9.0’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
CountGroups     8.155  0.429   8.958
FlowSOM         6.465  0.592   7.249
ProcessGatingML 5.832  0.400   6.887
PlotPies        5.815  0.286   6.406
ReadInput       4.123  0.385   5.290
* 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: OK

* installing *source* package ‘FlowSOM’ ...
** libs
clang -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 -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 /Users/biocbuild/bbs-3.6-bioc/meat/FlowSOM.Rcheck/FlowSOM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FlowSOM)

name	user	system	elapsed
AggregateFlowFrames	0.941	0.020	1.124
BuildMST	1.464	0.040	1.726
BuildSOM	2.335	0.046	2.710
CountGroups	8.155	0.429	8.958
FMeasure	0.003	0.000	0.003
FlowSOM	6.465	0.592	7.249
FlowSOMSubset	3.182	0.300	3.565
MetaClustering	3.088	0.348	3.568
NewData	2.792	0.318	3.186
PlotCenters	1.298	0.059	1.385
PlotClusters2D	1.121	0.060	1.218
PlotGroups	0.001	0.001	0.001
PlotMarker	1.015	0.060	1.106
PlotNode	3.168	0.314	3.715
PlotNumbers	1.302	0.033	1.578
PlotPies	5.815	0.286	6.406
PlotStars	1.127	0.054	1.194
PlotVariable	1.484	0.039	1.870
ProcessGatingML	5.832	0.400	6.887
Purity	0.001	0.000	0.002
QueryStarPlot	2.299	0.092	2.538
ReadInput	4.123	0.385	5.290
UpdateNodeSize	1.504	0.063	1.655
metaClustering_consensus	2.783	0.298	3.309

BioC 3.6: CHECK report for FlowSOM on veracruz1

Summary

Command output