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This page was generated on 2021-12-01 17:18:15 -0500 (Wed, 01 Dec 2021).

CHECK results for CytoTree on machv2

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: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoTree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoTree_1.4.0.tar.gz
StartedAt: 2021-11-30 15:29:45 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 15:37:53 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 487.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoTree.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoTree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoTree_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CytoTree.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
runCluster         17.803  0.057  17.885
plot2D             14.513  0.239  14.801
runMclust          13.502  0.024  13.533
plotCluster         8.285  0.048   8.343
runUMAP             8.047  0.114   8.182
plotPseudotimeTraj  6.495  0.074   6.577
plotPieCluster      5.372  0.113   5.492
runTSNE             5.274  0.018   5.301
* 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
  ‘/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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoTree
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CytoTree’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c jaccard_coeff.cpp -o jaccard_coeff.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CytoTree.so RcppExports.o jaccard_coeff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-CytoTree/00new/CytoTree/libs
** 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
** 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’
** checking absolute paths in shared objects and dynamic libraries
** 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
* DONE (CytoTree)

Tests output


Example timings

CytoTree.Rcheck/CytoTree-Ex.timings

nameusersystemelapsed
CytoTree-package0.0010.0000.001
Rphenograph3.6550.0183.675
buildTree0.2090.0130.258
constraintMatrix0.0510.0010.052
correctBatchCYT1.7600.0221.786
createCYT0.1550.0050.161
defLeafCells0.0280.0020.030
defRootCells0.0280.0010.029
fetchCell0.0320.0030.034
fetchClustMeta0.0530.0040.058
fetchPlotMeta0.0480.0070.056
find_neighbors0.0020.0000.003
gatingMatrix0.0240.0010.025
plot2D14.513 0.23914.801
plot3D0.0640.0040.068
plotBranchHeatmap0.3460.0120.359
plotCluster8.2850.0488.343
plotClusterHeatmap0.3350.0090.345
plotHeatmap0.9220.0440.970
plotMarkerDensity0.0000.0010.000
plotPieCluster5.3720.1135.492
plotPieTree0.8350.0120.849
plotPseudotimeDensity1.3870.0111.400
plotPseudotimeTraj6.4950.0746.577
plotTree1.9820.0101.997
plotViolin4.8770.0654.946
processingCluster0.7240.0380.766
runClara0.0680.0010.069
runCluster17.803 0.05717.885
runDiff0.0960.0030.100
runDiffusionMap0.4210.0320.454
runExprsExtract0.0180.0000.018
runExprsMerge0.0940.0020.095
runFastPCA0.0330.0010.033
runKmeans0.0250.0010.026
runMclust13.502 0.02413.533
runPhenograph4.3530.0114.368
runPseudotime1.8370.0401.882
runSOM0.0490.0030.052
runTSNE5.2740.0185.301
runUMAP8.0470.1148.182
runWalk0.4180.0070.425
show-CYT-method0.0200.0020.021
subsetCYT0.0250.0020.027
updateClustMeta0.0430.0020.046
updatePlotMeta0.0310.0030.035