Package: FlowSOM

Version: 1.15.1

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_1.15.1.tar.gz

StartedAt: 2019-04-09 00:55:44 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:57:55 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 131.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FlowSOM.Rcheck

Warnings: 1

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### Running command:
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###   /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_1.15.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.15.1’
* 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-3.9-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 ... 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 or elapsed time > 5s
                 user system elapsed
FlowSOM         8.935  0.871   9.882
CountGroups     8.041  0.598   8.731
ProcessGatingML 6.003  0.537   6.603
PlotPies        5.408  0.408   5.894
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FlowSOM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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
* DONE (FlowSOM)

name	user	system	elapsed
AggregateFlowFrames	0.236	0.015	0.252
BuildMST	1.320	0.094	1.419
BuildSOM	1.838	0.090	1.939
CountGroups	8.041	0.598	8.731
FMeasure	0.002	0.000	0.003
FlowSOM	8.935	0.871	9.882
FlowSOMSubset	4.032	0.399	4.474
MetaClustering	4.010	0.417	4.477
NewData	3.965	0.357	4.372
PlotCenters	1.504	0.079	1.590
PlotClusters2D	1.328	0.085	1.422
PlotGroups	0	0	0
PlotMarker	1.355	0.071	1.429
PlotNode	3.824	0.356	4.204
PlotNumbers	1.262	0.062	1.333
PlotPies	5.408	0.408	5.894
PlotStars	1.386	0.062	1.461
PlotVariable	1.473	0.067	1.549
ProcessGatingML	6.003	0.537	6.603
Purity	0.001	0.000	0.002
QueryStarPlot	2.847	0.116	2.997
ReadInput	4.300	0.412	4.751
UpdateNodeSize	1.670	0.074	1.760
metaClustering_consensus	3.153	0.390	3.580