Sofie Van Gassen
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/FlowSOM |
| Branch: RELEASE_3_8 |
| Last Commit: 9c69691 |
| Last Changed Date: 2019-01-04 13:32:51 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:13 -0400 (Tue, 16 Apr 2019).
| Package 546/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FlowSOM 1.14.1 Sofie Van Gassen
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: FlowSOM |
| Version: 1.14.1 |
| 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_1.14.1.tar.gz |
| StartedAt: 2019-04-15 23:59:24 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-16 00:01:36 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 131.8 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_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/FlowSOM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.1’
* 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-3.8-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 9.300 0.898 10.281
CountGroups 8.042 0.621 8.717
ProcessGatingML 6.064 0.537 6.658
PlotPies 5.279 0.395 5.715
FlowSOMSubset 4.893 0.397 5.489
* 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-3.8-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
FlowSOM.Rcheck/00install.out
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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/3.5/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/3.5/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)
FlowSOM.Rcheck/FlowSOM-Ex.timings
| name | user | system | elapsed | |
| AggregateFlowFrames | 0.244 | 0.018 | 0.266 | |
| BuildMST | 1.459 | 0.101 | 1.572 | |
| BuildSOM | 1.920 | 0.080 | 2.016 | |
| CountGroups | 8.042 | 0.621 | 8.717 | |
| FMeasure | 0.002 | 0.000 | 0.002 | |
| FlowSOM | 9.300 | 0.898 | 10.281 | |
| FlowSOMSubset | 4.893 | 0.397 | 5.489 | |
| MetaClustering | 3.989 | 0.392 | 4.424 | |
| NewData | 3.831 | 0.352 | 4.232 | |
| PlotCenters | 1.504 | 0.074 | 1.589 | |
| PlotClusters2D | 1.313 | 0.076 | 1.408 | |
| PlotGroups | 0.001 | 0.000 | 0.001 | |
| PlotMarker | 1.303 | 0.062 | 1.374 | |
| PlotNode | 3.489 | 0.357 | 3.862 | |
| PlotNumbers | 1.427 | 0.069 | 1.508 | |
| PlotPies | 5.279 | 0.395 | 5.715 | |
| PlotStars | 1.433 | 0.076 | 1.523 | |
| PlotVariable | 1.213 | 0.080 | 1.301 | |
| ProcessGatingML | 6.064 | 0.537 | 6.658 | |
| Purity | 0.001 | 0.000 | 0.002 | |
| QueryStarPlot | 2.555 | 0.133 | 2.711 | |
| ReadInput | 4.003 | 0.467 | 4.570 | |
| UpdateNodeSize | 1.462 | 0.083 | 1.555 | |
| metaClustering_consensus | 3.066 | 0.342 | 3.430 | |