Package: FlowSOM

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FlowSOM_1.10.0.tar.gz

StartedAt: 2018-04-12 03:50:01 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:52:13 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 131.8 seconds

RetCode: 0

Status:  OK

CheckDir: FlowSOM.Rcheck

Warnings: 0

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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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/FlowSOM.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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
FlowSOM         8.624  0.735  10.030
CountGroups     8.573  0.479  10.213
ProcessGatingML 5.564  0.498   6.148
PlotPies        5.546  0.376   5.979
* 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	0.951	0.021	1.099
BuildMST	1.494	0.046	1.743
BuildSOM	2.285	0.050	2.437
CountGroups	8.573	0.479	10.213
FMeasure	0.003	0.000	0.003
FlowSOM	8.624	0.735	10.030
FlowSOMSubset	3.485	0.370	4.087
MetaClustering	3.441	0.334	4.249
NewData	3.180	0.320	3.582
PlotCenters	1.163	0.063	1.253
PlotClusters2D	0.981	0.044	1.038
PlotGroups	0.001	0.000	0.001
PlotMarker	0.951	0.027	0.988
PlotNode	2.996	0.307	3.367
PlotNumbers	1.243	0.059	1.331
PlotPies	5.546	0.376	5.979
PlotStars	1.167	0.053	1.233
PlotVariable	1.111	0.061	1.187
ProcessGatingML	5.564	0.498	6.148
Purity	0.002	0.000	0.002
QueryStarPlot	2.231	0.094	2.362
ReadInput	3.468	0.400	3.961
UpdateNodeSize	1.531	0.060	1.619
metaClustering_consensus	2.915	0.350	3.337