| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:34 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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To the developers/maintainers of the FlowSOM package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 718/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.9.0 (landing page) Sofie Van Gassen
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: FlowSOM |
| Version: 2.9.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FlowSOM_2.9.0.tar.gz |
| StartedAt: 2023-05-30 07:32:00 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 07:48:15 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 974.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FlowSOM_2.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FlowSOM.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.9.0’
* package encoding: UTF-8
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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
PlotManualBars: no visible binding for global variable ‘MC’
PlotManualBars: no visible binding for global variable ‘Manual’
Undefined global functions or variables:
MC Manual
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PlotDimRed 89.545 0.221 89.718
FlowSOMmary 80.655 0.475 80.956
UpdateMetaclusters 22.191 0.760 22.959
PlotOutliers 21.780 0.032 21.813
PlotMarker 21.629 0.104 21.734
PlotStars 18.973 0.048 19.021
GroupStats 17.570 0.020 17.591
FlowSOM 16.292 0.116 16.409
PlotGroups 15.094 0.056 15.151
query_multiple 12.368 0.480 12.848
AddAnnotation 12.154 0.172 12.332
QueryMultiple 11.561 0.028 11.589
PlotManualBars 10.775 0.024 10.800
Plot2DScatters 10.676 0.040 10.682
GetFlowJoLabels 10.150 0.108 10.260
QueryStarPlot 9.138 0.116 9.255
PlotNode 9.173 0.072 9.246
PlotVariable 9.051 0.040 9.091
SaveClustersToFCS 8.556 0.287 8.845
PlotPies 8.714 0.028 8.742
PlotNumbers 8.712 0.020 8.734
CountGroups 8.628 0.096 8.724
PlotFlowSOM 7.771 0.088 7.859
UpdateNodeSize 7.604 0.188 7.793
GetFeatures 7.360 0.044 7.404
PlotLabels 7.102 0.048 7.151
NMetaclusters 7.010 0.087 7.098
TestOutliers 6.877 0.200 7.078
MetaclusterMFIs 7.038 0.032 7.071
PlotOverview2D 6.757 0.072 6.830
NClusters 6.655 0.024 6.680
MetaclusterCVs 6.383 0.048 6.432
print.FlowSOM 6.258 0.132 6.390
GetMFIs 6.248 0.104 6.352
GetMetaclusterCVs 6.317 0.008 6.325
GetPercentages 6.188 0.016 6.205
FlowSOMSubset 6.073 0.088 6.160
GetMetaclusterPercentagesPositive 6.135 0.024 6.159
GetClusterPercentagesPositive 6.049 0.108 6.158
GetMetaclusterMFIs 6.064 0.020 6.085
GetMetaclusters 6.060 0.008 6.068
GetCounts 5.784 0.100 5.885
GetClusterMFIs 5.732 0.148 5.881
GetClusters 5.783 0.032 5.815
ReadInput 5.340 0.228 5.568
NewData 5.079 0.012 5.091
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘FlowSOM.Rnw’ using ‘latin-9’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c som.c -o som.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-FlowSOM/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FlowSOM)
FlowSOM.Rcheck/FlowSOM-Ex.timings
| name | user | system | elapsed | |
| AddAnnotation | 12.154 | 0.172 | 12.332 | |
| AggregateFlowFrames | 0.085 | 0.004 | 0.089 | |
| BuildMST | 1.952 | 0.028 | 1.980 | |
| BuildSOM | 2.050 | 0.032 | 2.082 | |
| CountGroups | 8.628 | 0.096 | 8.724 | |
| FMeasure | 0.002 | 0.000 | 0.002 | |
| FlowSOM | 16.292 | 0.116 | 16.409 | |
| FlowSOMSubset | 6.073 | 0.088 | 6.160 | |
| FlowSOMmary | 80.655 | 0.475 | 80.956 | |
| GetChannels | 0.035 | 0.000 | 0.035 | |
| GetClusterMFIs | 5.732 | 0.148 | 5.881 | |
| GetClusterPercentagesPositive | 6.049 | 0.108 | 6.158 | |
| GetClusters | 5.783 | 0.032 | 5.815 | |
| GetCounts | 5.784 | 0.100 | 5.885 | |
| GetFeatures | 7.360 | 0.044 | 7.404 | |
| GetFlowJoLabels | 10.150 | 0.108 | 10.260 | |
| GetMFIs | 6.248 | 0.104 | 6.352 | |
| GetMarkers | 0.037 | 0.000 | 0.037 | |
| GetMetaclusterCVs | 6.317 | 0.008 | 6.325 | |
| GetMetaclusterMFIs | 6.064 | 0.020 | 6.085 | |
| GetMetaclusterPercentagesPositive | 6.135 | 0.024 | 6.159 | |
| GetMetaclusters | 6.060 | 0.008 | 6.068 | |
| GetPercentages | 6.188 | 0.016 | 6.205 | |
| GroupStats | 17.570 | 0.020 | 17.591 | |
| Initialize_KWSP | 0.007 | 0.000 | 0.007 | |
| Initialize_PCA | 0.002 | 0.000 | 0.001 | |
| MetaClustering | 4.603 | 0.012 | 4.615 | |
| MetaclusterCVs | 6.383 | 0.048 | 6.432 | |
| MetaclusterMFIs | 7.038 | 0.032 | 7.071 | |
| NClusters | 6.655 | 0.024 | 6.680 | |
| NMetaclusters | 7.010 | 0.087 | 7.098 | |
| NewData | 5.079 | 0.012 | 5.091 | |
| Plot2DScatters | 10.676 | 0.040 | 10.682 | |
| PlotCenters | 2.249 | 0.012 | 2.262 | |
| PlotClusters2D | 1.801 | 0.012 | 1.813 | |
| PlotDimRed | 89.545 | 0.221 | 89.718 | |
| PlotFileScatters | 0.983 | 0.040 | 1.023 | |
| PlotFlowSOM | 7.771 | 0.088 | 7.859 | |
| PlotGroups | 15.094 | 0.056 | 15.151 | |
| PlotLabels | 7.102 | 0.048 | 7.151 | |
| PlotManualBars | 10.775 | 0.024 | 10.800 | |
| PlotMarker | 21.629 | 0.104 | 21.734 | |
| PlotNode | 9.173 | 0.072 | 9.246 | |
| PlotNumbers | 8.712 | 0.020 | 8.734 | |
| PlotOutliers | 21.780 | 0.032 | 21.813 | |
| PlotOverview2D | 6.757 | 0.072 | 6.830 | |
| PlotPies | 8.714 | 0.028 | 8.742 | |
| PlotSD | 2.934 | 0.012 | 2.946 | |
| PlotStars | 18.973 | 0.048 | 19.021 | |
| PlotVariable | 9.051 | 0.040 | 9.091 | |
| Purity | 0.002 | 0.000 | 0.001 | |
| QueryMultiple | 11.561 | 0.028 | 11.589 | |
| QueryStarPlot | 9.138 | 0.116 | 9.255 | |
| ReadInput | 5.340 | 0.228 | 5.568 | |
| SaveClustersToFCS | 8.556 | 0.287 | 8.845 | |
| TestOutliers | 6.877 | 0.200 | 7.078 | |
| UpdateMetaclusters | 22.191 | 0.760 | 22.959 | |
| UpdateNodeSize | 7.604 | 0.188 | 7.793 | |
| get_channels | 0.039 | 0.000 | 0.039 | |
| get_markers | 0.034 | 0.004 | 0.038 | |
| metaClustering_consensus | 3.960 | 0.084 | 4.044 | |
| plotStarLegend | 0.442 | 0.004 | 0.446 | |
| print.FlowSOM | 6.258 | 0.132 | 6.390 | |
| query_multiple | 12.368 | 0.480 | 12.848 | |