| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:36 -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: 2023-04-12 06:20:28 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 06:31:51 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 683.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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 Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* 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 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 49.212 0.376 49.589
PlotDimRed 46.983 0.048 47.033
PlotMarker 18.489 0.041 18.531
UpdateMetaclusters 16.980 0.076 17.056
PlotOutliers 16.277 0.080 16.358
PlotStars 14.098 0.044 14.143
GroupStats 13.344 0.131 13.477
PlotGroups 11.934 0.056 11.990
FlowSOM 11.619 0.136 11.755
query_multiple 8.930 0.000 8.931
AddAnnotation 8.457 0.196 8.654
QueryMultiple 8.613 0.012 8.624
PlotManualBars 8.495 0.050 8.545
GetFlowJoLabels 7.667 0.117 7.783
Plot2DScatters 7.713 0.068 7.781
PlotNode 7.136 0.004 7.140
PlotNumbers 6.835 0.008 6.843
PlotVariable 6.707 0.032 6.742
PlotFlowSOM 6.632 0.100 6.732
QueryStarPlot 6.590 0.052 6.642
PlotPies 6.484 0.076 6.560
MetaclusterMFIs 5.880 0.064 5.944
NClusters 5.841 0.064 5.906
GetFeatures 5.883 0.015 5.911
CountGroups 5.767 0.124 5.891
TestOutliers 5.746 0.008 5.754
NMetaclusters 5.597 0.020 5.618
PlotLabels 5.469 0.004 5.472
MetaclusterCVs 5.277 0.048 5.328
GetMFIs 5.245 0.019 5.264
UpdateNodeSize 5.225 0.008 5.233
GetMetaclusterMFIs 5.129 0.008 5.137
PlotOverview2D 5.086 0.008 5.095
GetPercentages 5.043 0.040 5.083
SaveClustersToFCS 5.062 0.016 5.078
* 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’ 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 | 8.457 | 0.196 | 8.654 | |
| AggregateFlowFrames | 0.075 | 0.004 | 0.079 | |
| BuildMST | 1.087 | 0.012 | 1.099 | |
| BuildSOM | 1.147 | 0.063 | 1.212 | |
| CountGroups | 5.767 | 0.124 | 5.891 | |
| FMeasure | 0.001 | 0.000 | 0.001 | |
| FlowSOM | 11.619 | 0.136 | 11.755 | |
| FlowSOMSubset | 4.449 | 0.083 | 4.534 | |
| FlowSOMmary | 49.212 | 0.376 | 49.589 | |
| GetChannels | 0.030 | 0.001 | 0.030 | |
| GetClusterMFIs | 4.330 | 0.055 | 4.386 | |
| GetClusterPercentagesPositive | 3.971 | 0.000 | 3.972 | |
| GetClusters | 4.171 | 0.055 | 4.227 | |
| GetCounts | 4.383 | 0.033 | 4.414 | |
| GetFeatures | 5.883 | 0.015 | 5.911 | |
| GetFlowJoLabels | 7.667 | 0.117 | 7.783 | |
| GetMFIs | 5.245 | 0.019 | 5.264 | |
| GetMarkers | 0.027 | 0.001 | 0.027 | |
| GetMetaclusterCVs | 4.902 | 0.000 | 4.903 | |
| GetMetaclusterMFIs | 5.129 | 0.008 | 5.137 | |
| GetMetaclusterPercentagesPositive | 4.868 | 0.007 | 4.876 | |
| GetMetaclusters | 4.943 | 0.053 | 4.995 | |
| GetPercentages | 5.043 | 0.040 | 5.083 | |
| GroupStats | 13.344 | 0.131 | 13.477 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.004 | |
| Initialize_PCA | 0.001 | 0.000 | 0.001 | |
| MetaClustering | 3.172 | 0.044 | 3.215 | |
| MetaclusterCVs | 5.277 | 0.048 | 5.328 | |
| MetaclusterMFIs | 5.880 | 0.064 | 5.944 | |
| NClusters | 5.841 | 0.064 | 5.906 | |
| NMetaclusters | 5.597 | 0.020 | 5.618 | |
| NewData | 3.863 | 0.012 | 3.874 | |
| Plot2DScatters | 7.713 | 0.068 | 7.781 | |
| PlotCenters | 1.039 | 0.016 | 1.055 | |
| PlotClusters2D | 1.069 | 0.000 | 1.069 | |
| PlotDimRed | 46.983 | 0.048 | 47.033 | |
| PlotFileScatters | 0.768 | 0.004 | 0.773 | |
| PlotFlowSOM | 6.632 | 0.100 | 6.732 | |
| PlotGroups | 11.934 | 0.056 | 11.990 | |
| PlotLabels | 5.469 | 0.004 | 5.472 | |
| PlotManualBars | 8.495 | 0.050 | 8.545 | |
| PlotMarker | 18.489 | 0.041 | 18.531 | |
| PlotNode | 7.136 | 0.004 | 7.140 | |
| PlotNumbers | 6.835 | 0.008 | 6.843 | |
| PlotOutliers | 16.277 | 0.080 | 16.358 | |
| PlotOverview2D | 5.086 | 0.008 | 5.095 | |
| PlotPies | 6.484 | 0.076 | 6.560 | |
| PlotSD | 2.383 | 0.004 | 2.387 | |
| PlotStars | 14.098 | 0.044 | 14.143 | |
| PlotVariable | 6.707 | 0.032 | 6.742 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 8.613 | 0.012 | 8.624 | |
| QueryStarPlot | 6.590 | 0.052 | 6.642 | |
| ReadInput | 3.329 | 0.028 | 3.357 | |
| SaveClustersToFCS | 5.062 | 0.016 | 5.078 | |
| TestOutliers | 5.746 | 0.008 | 5.754 | |
| UpdateMetaclusters | 16.980 | 0.076 | 17.056 | |
| UpdateNodeSize | 5.225 | 0.008 | 5.233 | |
| get_channels | 0.028 | 0.000 | 0.027 | |
| get_markers | 0.028 | 0.000 | 0.028 | |
| metaClustering_consensus | 2.621 | 0.008 | 2.630 | |
| plotStarLegend | 0.329 | 0.004 | 0.333 | |
| print.FlowSOM | 4.427 | 0.016 | 4.443 | |
| query_multiple | 8.930 | 0.000 | 8.931 | |