Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-06 13:05:21 -0500 (Mon, 06 Dec 2021).

CHECK results for CytoTree on tokay2

To the developers/maintainers of the CytoTree package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoTree.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 444/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoTree 1.4.0  (landing page)
Yuting Dai
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/CytoTree
git_branch: RELEASE_3_14
git_last_commit: c190c92
git_last_commit_date: 2021-10-26 13:00:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  NO, package depends on 'destiny' which is not available
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'destiny' which is not available

Summary

Package: CytoTree
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CytoTree_1.4.0.tar.gz
StartedAt: 2021-12-05 18:55:19 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 19:04:25 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 545.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoTree.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CytoTree_1.4.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CytoTree.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CytoTree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoTree' version '1.4.0'
* 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 whether package 'CytoTree' 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/CytoTree/libs/i386/CytoTree.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/CytoTree/libs/x64/CytoTree.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
runCluster         13.57   0.00   13.56
runMclust           9.86   0.00    9.85
plot2D              8.72   0.45    9.17
runUMAP             6.12   0.18    6.31
plotPseudotimeTraj  5.42   0.05    5.47
plotCluster         5.33   0.10    5.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
runCluster 12.56   0.00   12.56
plot2D      8.89   0.10    8.99
runMclust   8.52   0.00    8.52
runUMAP     6.39   0.02    6.41
* 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/CytoTree.Rcheck/00check.log'
for details.



Installation output

CytoTree.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/CytoTree_1.4.0.tar.gz && rm -rf CytoTree.buildbin-libdir && mkdir CytoTree.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoTree.buildbin-libdir CytoTree_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CytoTree_1.4.0.zip && rm CytoTree_1.4.0.tar.gz CytoTree_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 13 1593k   13  211k    0     0   864k      0  0:00:01 --:--:--  0:00:01  864k
100 1593k  100 1593k    0     0  2827k      0 --:--:-- --:--:-- --:--:-- 2825k

install for i386

* installing *source* package 'CytoTree' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CytoTree.dll tmp.def RcppExports.o jaccard_coeff.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/CytoTree.buildbin-libdir/00LOCK-CytoTree/00new/CytoTree/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'flowCore' for requests: 'action', 'assign', 'Data', 'gate', 'tree' when loading 'flowUtils'
** help
*** installing help indices
  converting help for package 'CytoTree'
    finding HTML links ... done
    CYT-class                               html  
    CytoTree-package                        html  
    Rphenograph                             html  
    buildTree                               html  
    constraintMatrix                        html  
    correctBatchCYT                         html  
    createCYT                               html  
    defLeafCells                            html  
    defRootCells                            html  
    fetchCell                               html  
    fetchClustMeta                          html  
    fetchPlotMeta                           html  
    find_neighbors                          html  
    gatingMatrix                            html  
    plot2D                                  html  
    plot3D                                  html  
    plotBranchHeatmap                       html  
    plotCluster                             html  
    plotClusterHeatmap                      html  
    plotHeatmap                             html  
    plotMarkerDensity                       html  
    plotPieCluster                          html  
    plotPieTree                             html  
    plotPseudotimeDensity                   html  
    plotPseudotimeTraj                      html  
    plotTrajHeatmap                         html  
    plotTree                                html  
    plotViolin                              html  
    processingCluster                       html  
    runClara                                html  
    runCluster                              html  
    runDiff                                 html  
    runDiffusionMap                         html  
    runExprsExtract                         html  
    runExprsMerge                           html  
    runFastPCA                              html  
    runHclust                               html  
    runKNN                                  html  
    runKmeans                               html  
    runMclust                               html  
    runPhenograph                           html  
    runPseudotime                           html  
    runSOM                                  html  
    finding level-2 HTML links ... done

    runTSNE                                 html  
    runUMAP                                 html  
    runWalk                                 html  
    show-CYT-method                         html  
    subsetCYT                               html  
    updateClustMeta                         html  
    updatePlotMeta                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'flowCore' for requests: 'action', 'assign', 'Data', 'gate', 'tree' when loading 'flowUtils'
** testing if installed package can be loaded from final location
No methods found in package 'flowCore' for requests: 'action', 'assign', 'Data', 'gate', 'tree' when loading 'flowUtils'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CytoTree' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CytoTree.dll tmp.def RcppExports.o jaccard_coeff.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/CytoTree.buildbin-libdir/CytoTree/libs/x64
** testing if installed package can be loaded
No methods found in package 'flowCore' for requests: 'action', 'assign', 'Data', 'gate', 'tree' when loading 'flowUtils'
* MD5 sums
packaged installation of 'CytoTree' as CytoTree_1.4.0.zip
* DONE (CytoTree)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CytoTree' successfully unpacked and MD5 sums checked

Tests output


Example timings

CytoTree.Rcheck/examples_i386/CytoTree-Ex.timings

nameusersystemelapsed
CytoTree-package000
Rphenograph303
buildTree0.210.040.58
constraintMatrix0.040.020.06
correctBatchCYT0.800.020.81
createCYT0.370.012.78
defLeafCells0.050.000.05
defRootCells0.030.000.03
fetchCell0.030.000.03
fetchClustMeta0.050.000.05
fetchPlotMeta0.060.000.06
find_neighbors000
gatingMatrix0.030.000.03
plot2D8.720.459.17
plot3D0.060.000.06
plotBranchHeatmap0.30.00.3
plotCluster5.330.105.42
plotClusterHeatmap0.280.000.28
plotHeatmap1.000.031.03
plotMarkerDensity000
plotPieCluster3.800.173.97
plotPieTree0.520.000.52
plotPseudotimeDensity0.810.000.81
plotPseudotimeTraj5.420.055.47
plotTree1.130.251.37
plotViolin2.180.222.41
processingCluster0.850.001.90
runClara0.040.000.05
runCluster13.57 0.0013.56
runDiff0.060.000.07
runDiffusionMap0.330.060.39
runExprsExtract0.000.010.01
runExprsMerge0.090.070.16
runFastPCA0.030.000.03
runKmeans0.020.000.02
runMclust9.860.009.85
runPhenograph3.280.003.29
runPseudotime1.210.001.20
runSOM0.030.000.04
runTSNE3.40.03.4
runUMAP6.120.186.31
runWalk0.220.000.22
show-CYT-method000
subsetCYT0.010.000.02
updateClustMeta0.040.000.03
updatePlotMeta0.010.000.02

CytoTree.Rcheck/examples_x64/CytoTree-Ex.timings

nameusersystemelapsed
CytoTree-package000
Rphenograph3.350.033.40
buildTree0.120.000.13
constraintMatrix0.030.000.03
correctBatchCYT0.830.020.84
createCYT0.160.010.17
defLeafCells000
defRootCells000
fetchCell0.020.000.02
fetchClustMeta0.030.000.03
fetchPlotMeta0.030.000.03
find_neighbors000
gatingMatrix0.020.000.01
plot2D8.890.108.99
plot3D0.040.000.04
plotBranchHeatmap0.250.000.25
plotCluster4.970.014.98
plotClusterHeatmap0.220.000.22
plotHeatmap0.610.000.61
plotMarkerDensity000
plotPieCluster3.400.023.42
plotPieTree0.550.000.55
plotPseudotimeDensity0.840.000.85
plotPseudotimeTraj4.030.034.06
plotTree1.180.001.17
plotViolin3.220.013.24
processingCluster0.950.021.18
runClara0.050.000.05
runCluster12.56 0.0012.56
runDiff0.040.000.05
runDiffusionMap0.290.060.34
runExprsExtract0.030.000.03
runExprsMerge0.080.050.13
runFastPCA0.000.020.01
runKmeans0.010.000.02
runMclust8.520.008.52
runPhenograph3.640.003.64
runPseudotime0.500.030.53
runSOM0.020.000.02
runTSNE2.980.013.00
runUMAP6.390.026.41
runWalk0.240.000.23
show-CYT-method000
subsetCYT0.010.000.02
updateClustMeta0.020.000.01
updatePlotMeta000