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) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:20 -0400 (Thu, 06 May 2021).
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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 631/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 1.22.0 (landing page) Sofie Van Gassen
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: FlowSOM |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings FlowSOM_1.22.0.tar.gz |
| StartedAt: 2021-05-06 02:53:08 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:59:20 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 372.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings FlowSOM_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/FlowSOM/libs/i386/FlowSOM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/FlowSOM/libs/x64/FlowSOM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CountGroups 10.33 0.19 10.53
PlotOverview2D 5.54 3.99 9.53
FlowSOM 7.14 0.20 7.56
MetaclusterCVs 5.81 0.03 5.85
TestOutliers 5.55 0.06 5.61
MetaclusterMFIs 5.05 0.13 5.17
PlotLabels 5.04 0.06 5.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PlotOverview2D 7.00 4.28 11.30
CountGroups 10.08 0.13 10.20
FlowSOM 7.58 0.04 7.63
PlotPies 5.95 0.07 6.03
TestOutliers 5.11 0.11 5.22
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.Rcheck/00check.log'
for details.
FlowSOM.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/FlowSOM_1.22.0.tar.gz && rm -rf FlowSOM.buildbin-libdir && mkdir FlowSOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FlowSOM.buildbin-libdir FlowSOM_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL FlowSOM_1.22.0.zip && rm FlowSOM_1.22.0.tar.gz FlowSOM_1.22.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1157k 100 1157k 0 0 23.5M 0 --:--:-- --:--:-- --:--:-- 24.0M
install for i386
* installing *source* package 'FlowSOM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c som.c -o som.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o FlowSOM.dll tmp.def som.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.buildbin-libdir/00LOCK-FlowSOM/00new/FlowSOM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'FlowSOM'
finding HTML links ... done
AddFlowFrame html
AggregateFlowFrames html
BuildMST html
BuildSOM html
CountGroups html
Dist.MST html
FMeasure html
FlowSOM html
FlowSOMSubset html
GetCVs html
GetClusters html
GetFlowJoLabels html
finding level-2 HTML links ... done
GetMFIs html
GetMetaclusters html
Initialize_KWSP html
Initialize_PCA html
MapDataToCodes html
MetaClustering html
MetaclusterCVs html
MetaclusterMFIs html
NewData html
PlotCenters html
PlotClusters2D html
PlotGroups html
PlotLabels html
PlotMarker html
PlotNode html
PlotNumbers html
PlotOverview2D html
PlotPies html
PlotSD html
PlotStars html
PlotVariable html
Purity html
QueryStarPlot html
ReadInput html
SOM html
SaveClustersToFCS html
TestOutliers html
UpdateNodeSize html
computeBackgroundColor html
get_channels html
get_markers html
metaClustering_consensus html
plotStarLegend html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'FlowSOM' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c som.c -o som.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o FlowSOM.dll tmp.def som.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.buildbin-libdir/FlowSOM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FlowSOM' as FlowSOM_1.22.0.zip
* DONE (FlowSOM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'FlowSOM' successfully unpacked and MD5 sums checked
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FlowSOM.Rcheck/examples_i386/FlowSOM-Ex.timings
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FlowSOM.Rcheck/examples_x64/FlowSOM-Ex.timings
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