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This page was generated on 2024-03-28 11:39:16 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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

Package 743/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.11.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: devel
git_last_commit: 47d1347
git_last_commit_date: 2023-10-24 10:40:45 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for FlowSOM on lconway


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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: FlowSOM
Version: 2.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.11.0.tar.gz
StartedAt: 2024-03-27 21:12:28 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 21:24:21 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 713.2 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.11.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 whether 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) PlotDimRed.Rd:55: Lost braces
    55 | of the dimred default = function(dimred){dimred$Y}.}
       |                                         ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
FlowSOMmary                       68.290  2.756  71.570
PlotDimRed                        44.063  2.863  47.626
PlotMarker                        29.531  1.536  31.545
UpdateMetaclusters                26.345  1.666  28.388
PlotStars                         21.310  1.350  22.977
PlotOutliers                      20.517  1.041  21.846
GroupStats                        20.021  1.205  21.553
query_multiple                    17.424  0.661  18.249
QueryMultiple                     17.302  0.644  18.202
PlotGroups                        16.377  1.352  18.046
FlowSOM                           14.702  1.208  16.107
Plot2DScatters                    13.058  0.981  14.281
AddAnnotation                     13.208  0.785  14.139
QueryStarPlot                     12.168  0.456  12.835
PlotNumbers                        9.811  1.115  11.105
UpdateNodeSize                    10.387  0.381  10.863
GetFlowJoLabels                    9.735  0.747  10.589
PlotNode                           9.449  0.952  10.547
PlotVariable                       9.345  0.987  10.506
PlotPies                           8.745  0.892   9.832
PlotManualBars                     8.611  1.012   9.779
PlotFlowSOM                        7.721  0.878   8.736
PlotLabels                         6.547  0.828   7.519
SaveClustersToFCS                  6.300  1.003   7.407
CountGroups                        6.559  0.647   7.303
GetFeatures                        6.151  0.500   6.723
NClusters                          5.616  1.020   6.719
MetaclusterMFIs                    5.539  0.881   6.505
NMetaclusters                      5.321  0.937   6.332
TestOutliers                       5.357  0.792   6.251
GetPercentages                     5.295  0.765   6.170
GetMFIs                            5.273  0.753   6.110
MetaclusterCVs                     5.184  0.745   6.041
GetMetaclusters                    4.976  0.841   5.937
PlotOverview2D                     5.058  0.759   5.910
GetMetaclusterPercentagesPositive  4.988  0.708   5.742
GetMetaclusterMFIs                 4.876  0.750   5.686
print.FlowSOM                      4.895  0.704   5.656
GetMetaclusterCVs                  4.753  0.731   5.564
GetClusters                        4.627  0.629   5.316
GetCounts                          4.710  0.530   5.316
NewData                            4.659  0.580   5.334
GetClusterMFIs                     4.579  0.539   5.185
FlowSOMSubset                      4.629  0.479   5.168
GetClusterPercentagesPositive      4.521  0.506   5.084
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output


Example timings

FlowSOM.Rcheck/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation13.208 0.78514.139
AggregateFlowFrames0.1100.0070.117
BuildMST1.4720.1071.599
BuildSOM1.5910.1101.726
CountGroups6.5590.6477.303
FMeasure0.0020.0000.002
FlowSOM14.702 1.20816.107
FlowSOMSubset4.6290.4795.168
FlowSOMmary68.290 2.75671.570
GetChannels0.0440.0030.048
GetClusterMFIs4.5790.5395.185
GetClusterPercentagesPositive4.5210.5065.084
GetClusters4.6270.6295.316
GetCounts4.7100.5305.316
GetFeatures6.1510.5006.723
GetFlowJoLabels 9.735 0.74710.589
GetMFIs5.2730.7536.110
GetMarkers0.0480.0030.051
GetMetaclusterCVs4.7530.7315.564
GetMetaclusterMFIs4.8760.7505.686
GetMetaclusterPercentagesPositive4.9880.7085.742
GetMetaclusters4.9760.8415.937
GetPercentages5.2950.7656.170
GroupStats20.021 1.20521.553
Initialize_KWSP0.0050.0010.006
Initialize_PCA0.0010.0010.001
MetaClustering3.8440.7134.671
MetaclusterCVs5.1840.7456.041
MetaclusterMFIs5.5390.8816.505
NClusters5.6161.0206.719
NMetaclusters5.3210.9376.332
NewData4.6590.5805.334
Plot2DScatters13.058 0.98114.281
PlotCenters1.3140.0881.426
PlotClusters2D1.2950.1191.435
PlotDimRed44.063 2.86347.626
PlotFileScatters1.2930.0801.392
PlotFlowSOM7.7210.8788.736
PlotGroups16.377 1.35218.046
PlotLabels6.5470.8287.519
PlotManualBars8.6111.0129.779
PlotMarker29.531 1.53631.545
PlotNode 9.449 0.95210.547
PlotNumbers 9.811 1.11511.105
PlotOutliers20.517 1.04121.846
PlotOverview2D5.0580.7595.910
PlotPies8.7450.8929.832
PlotSD3.0580.2513.351
PlotStars21.310 1.35022.977
PlotVariable 9.345 0.98710.506
Purity0.0010.0000.001
QueryMultiple17.302 0.64418.202
QueryStarPlot12.168 0.45612.835
ReadInput3.7970.7164.619
SaveClustersToFCS6.3001.0037.407
TestOutliers5.3570.7926.251
UpdateMetaclusters26.345 1.66628.388
UpdateNodeSize10.387 0.38110.863
get_channels0.0430.0030.046
get_markers0.0430.0030.047
metaClustering_consensus2.8150.6313.487
plotStarLegend1.0250.0241.060
print.FlowSOM4.8950.7045.656
query_multiple17.424 0.66118.249