Sofie Van Gassen
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/FlowSOM |
| git_branch: RELEASE_3_14 |
| git_last_commit: 44e9c9b |
| git_last_commit_date: 2021-10-26 12:18:07 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:34 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the FlowSOM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FlowSOM.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 670/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.2.0 (landing page) Sofie Van Gassen
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FlowSOM |
| Version: 2.2.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FlowSOM_2.2.0.tar.gz |
| StartedAt: 2022-04-12 19:48:06 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 20:11:15 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1389.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FlowSOM_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.2.0'
* 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/FlowSOM/libs/i386/FlowSOM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-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
FlowSOMmary 57.33 0.69 58.09
PlotDimRed 43.97 0.26 44.30
UpdateMetaclusters 23.53 0.09 29.61
PlotMarker 21.77 0.16 22.01
GroupStats 15.67 0.26 24.30
PlotGroups 15.75 0.09 16.12
FlowSOM 13.95 0.24 14.19
AddAnnotation 10.89 0.08 11.20
UpdateNodeSize 9.49 0.13 48.78
QueryMultiple 8.92 0.07 8.99
query_multiple 8.71 0.02 8.73
PlotNode 8.59 0.03 49.28
PlotStars 8.15 0.04 12.36
PlotFlowSOM 7.88 0.08 23.42
GetFlowJoLabels 7.61 0.12 10.05
PlotManualBars 7.57 0.14 10.22
PlotNumbers 7.56 0.02 31.32
PlotPies 7.25 0.18 7.47
QueryStarPlot 7.25 0.06 21.08
CountGroups 7.10 0.20 7.29
Plot2DScatters 5.91 0.58 6.49
TestOutliers 6.03 0.07 64.53
PlotLabels 5.48 0.00 5.50
PlotVariable 5.29 0.03 5.32
GetFeatures 5.20 0.08 5.28
PlotOverview2D 4.36 0.08 70.68
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
FlowSOMmary 63.34 1.06 64.42
PlotDimRed 47.23 0.15 47.40
UpdateMetaclusters 26.32 0.05 26.38
PlotMarker 23.25 0.07 23.36
GroupStats 17.61 0.14 17.78
FlowSOM 15.79 0.11 15.89
PlotGroups 14.71 0.09 14.81
QueryMultiple 13.05 0.08 13.17
PlotNode 11.42 0.05 11.50
UpdateNodeSize 11.06 0.08 11.14
AddAnnotation 10.95 0.10 11.04
query_multiple 10.61 0.00 10.61
QueryStarPlot 8.69 0.03 8.72
PlotStars 8.59 0.02 8.62
Plot2DScatters 7.81 0.64 8.47
PlotFlowSOM 8.19 0.05 8.24
PlotManualBars 7.54 0.15 7.69
GetFlowJoLabels 7.53 0.10 8.93
PlotNumbers 7.27 0.00 7.26
PlotPies 6.93 0.04 6.98
PlotVariable 6.89 0.06 6.96
CountGroups 6.66 0.20 11.05
SaveClustersToFCS 6.29 0.01 6.31
TestOutliers 6.25 0.03 6.28
PlotLabels 5.65 0.03 5.67
GetMetaclusters 5.29 0.01 5.30
MetaclusterMFIs 5.22 0.08 5.29
NMetaclusters 5.20 0.06 5.26
print.FlowSOM 5.13 0.03 5.16
NClusters 5.03 0.02 5.05
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.14-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://155.52.207.166/BBS/3.14/bioc/src/contrib/FlowSOM_2.2.0.tar.gz && rm -rf FlowSOM.buildbin-libdir && mkdir FlowSOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FlowSOM.buildbin-libdir FlowSOM_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FlowSOM_2.2.0.zip && rm FlowSOM_2.2.0.tar.gz FlowSOM_2.2.0.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
34 1197k 34 419k 0 0 1557k 0 --:--:-- --:--:-- --:--:-- 1558k
100 1197k 100 1197k 0 0 2428k 0 --:--:-- --:--:-- --:--:-- 2428k
install for i386
* installing *source* package 'FlowSOM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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
AddAnnotation html
AddBackground html
AddFlowFrame html
AddLabels html
AddMST html
AddNodes html
AddPies html
AddScale html
AddStars html
AddStarsPies html
AggregateFlowFrames html
AutoMaxNodeSize html
BuildMST html
BuildSOM html
CountGroups html
Dist.MST html
FMeasure html
FlowSOM html
FlowSOMSubset html
FlowSOM_colors html
FlowSOMmary html
GetCVs html
GetChannels html
GetClusterCVs html
GetClusterMFIs html
GetClusters html
GetCounts html
GetFeatures html
GetFlowJoLabels html
finding level-2 HTML links ... done
GetMFIs html
GetMarkers html
GetMetaclusterCVs html
GetMetaclusterMFIs html
GetMetaclusters html
GetPercentages html
GroupStats html
Initialize_KWSP html
Initialize_PCA html
ManualVector html
MapDataToCodes html
MetaClustering html
MetaclusterCVs html
MetaclusterMFIs html
NClusters html
NMetaclusters html
NewData html
ParseArcs html
ParseEdges html
ParseLayout html
ParseNodeSize html
ParseQuery html
ParseSD html
Plot2DScatters html
PlotCenters html
PlotClusters2D html
PlotDimRed html
PlotFileScatters html
PlotFlowSOM html
PlotGroups html
PlotLabels html
PlotManualBars html
PlotMarker html
PlotNode html
PlotNumbers html
PlotOverview2D html
PlotPies html
PlotSD html
PlotStars html
PlotVariable html
Purity html
QueryMultiple html
QueryStarPlot html
ReadInput html
SOM html
SaveClustersToFCS html
ScaleStarHeights html
TestOutliers html
UpdateFlowSOM html
UpdateMetaclusters html
UpdateNodeSize html
get_channels html
get_markers html
gg_color_hue html
metaClustering_consensus html
pipe html
plotStarLegend html
print.FlowSOM html
query_multiple 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-3~1.14-/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.buildbin-libdir/FlowSOM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FlowSOM' as FlowSOM_2.2.0.zip
* DONE (FlowSOM)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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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