| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:24 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 719/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.7.10 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: FlowSOM |
| Version: 2.7.10 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings FlowSOM_2.7.10.tar.gz |
| StartedAt: 2023-04-11 20:22:04 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 20:32:53 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 648.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings FlowSOM_2.7.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FlowSOM.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 ‘2.7.10’
* 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) 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
FlowSOMmary 47.007 0.288 47.296
PlotDimRed 43.448 0.084 43.532
PlotMarker 17.975 0.080 18.055
PlotOutliers 15.743 0.020 15.763
UpdateMetaclusters 15.337 0.088 15.425
PlotStars 14.104 0.064 14.168
GroupStats 12.293 0.092 12.385
PlotGroups 11.078 0.024 11.105
FlowSOM 10.911 0.112 11.025
AddAnnotation 8.214 0.192 8.408
QueryMultiple 8.345 0.012 8.357
query_multiple 7.872 0.024 7.895
Plot2DScatters 7.684 0.028 7.685
PlotManualBars 7.508 0.084 7.593
GetFlowJoLabels 6.992 0.056 7.050
PlotVariable 6.803 0.048 6.852
PlotPies 6.273 0.095 6.369
QueryStarPlot 6.340 0.012 6.352
PlotNumbers 6.225 0.020 6.256
PlotNode 6.222 0.020 6.243
CountGroups 5.670 0.112 5.782
PlotFlowSOM 5.601 0.036 5.638
UpdateNodeSize 5.575 0.012 5.587
NMetaclusters 5.077 0.024 5.100
MetaclusterMFIs 5.054 0.008 5.063
GetFeatures 5.025 0.028 5.058
SaveClustersToFCS 5.012 0.028 5.040
NClusters 4.986 0.028 5.013
* 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-3.17-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c som.c -o som.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 | 8.214 | 0.192 | 8.408 | |
| AggregateFlowFrames | 0.073 | 0.011 | 0.085 | |
| BuildMST | 1.279 | 0.009 | 1.287 | |
| BuildSOM | 1.049 | 0.052 | 1.102 | |
| CountGroups | 5.670 | 0.112 | 5.782 | |
| FMeasure | 0.002 | 0.000 | 0.002 | |
| FlowSOM | 10.911 | 0.112 | 11.025 | |
| FlowSOMSubset | 4.113 | 0.055 | 4.169 | |
| FlowSOMmary | 47.007 | 0.288 | 47.296 | |
| GetChannels | 0.027 | 0.000 | 0.027 | |
| GetClusterMFIs | 3.873 | 0.036 | 3.909 | |
| GetClusterPercentagesPositive | 3.870 | 0.016 | 3.886 | |
| GetClusters | 4.364 | 0.012 | 4.376 | |
| GetCounts | 3.867 | 0.040 | 3.907 | |
| GetFeatures | 5.025 | 0.028 | 5.058 | |
| GetFlowJoLabels | 6.992 | 0.056 | 7.050 | |
| GetMFIs | 4.713 | 0.068 | 4.781 | |
| GetMarkers | 0.024 | 0.004 | 0.028 | |
| GetMetaclusterCVs | 4.530 | 0.012 | 4.542 | |
| GetMetaclusterMFIs | 4.349 | 0.008 | 4.357 | |
| GetMetaclusterPercentagesPositive | 4.448 | 0.012 | 4.464 | |
| GetMetaclusters | 4.784 | 0.004 | 4.788 | |
| GetPercentages | 4.321 | 0.012 | 4.333 | |
| GroupStats | 12.293 | 0.092 | 12.385 | |
| Initialize_KWSP | 0.003 | 0.000 | 0.004 | |
| Initialize_PCA | 0.001 | 0.000 | 0.001 | |
| MetaClustering | 3.305 | 0.024 | 3.330 | |
| MetaclusterCVs | 4.746 | 0.064 | 4.811 | |
| MetaclusterMFIs | 5.054 | 0.008 | 5.063 | |
| NClusters | 4.986 | 0.028 | 5.013 | |
| NMetaclusters | 5.077 | 0.024 | 5.100 | |
| NewData | 4.108 | 0.012 | 4.120 | |
| Plot2DScatters | 7.684 | 0.028 | 7.685 | |
| PlotCenters | 1.025 | 0.012 | 1.037 | |
| PlotClusters2D | 1.500 | 0.004 | 1.503 | |
| PlotDimRed | 43.448 | 0.084 | 43.532 | |
| PlotFileScatters | 0.690 | 0.016 | 0.707 | |
| PlotFlowSOM | 5.601 | 0.036 | 5.638 | |
| PlotGroups | 11.078 | 0.024 | 11.105 | |
| PlotLabels | 4.903 | 0.016 | 4.920 | |
| PlotManualBars | 7.508 | 0.084 | 7.593 | |
| PlotMarker | 17.975 | 0.080 | 18.055 | |
| PlotNode | 6.222 | 0.020 | 6.243 | |
| PlotNumbers | 6.225 | 0.020 | 6.256 | |
| PlotOutliers | 15.743 | 0.020 | 15.763 | |
| PlotOverview2D | 4.477 | 0.009 | 4.486 | |
| PlotPies | 6.273 | 0.095 | 6.369 | |
| PlotSD | 1.922 | 0.008 | 1.931 | |
| PlotStars | 14.104 | 0.064 | 14.168 | |
| PlotVariable | 6.803 | 0.048 | 6.852 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 8.345 | 0.012 | 8.357 | |
| QueryStarPlot | 6.340 | 0.012 | 6.352 | |
| ReadInput | 3.341 | 0.012 | 3.353 | |
| SaveClustersToFCS | 5.012 | 0.028 | 5.040 | |
| TestOutliers | 4.564 | 0.016 | 4.580 | |
| UpdateMetaclusters | 15.337 | 0.088 | 15.425 | |
| UpdateNodeSize | 5.575 | 0.012 | 5.587 | |
| get_channels | 0.024 | 0.004 | 0.027 | |
| get_markers | 0.027 | 0.000 | 0.027 | |
| metaClustering_consensus | 2.231 | 0.004 | 2.236 | |
| plotStarLegend | 0.327 | 0.004 | 0.330 | |
| print.FlowSOM | 4.08 | 0.08 | 4.16 | |
| query_multiple | 7.872 | 0.024 | 7.895 | |