Back to Multiple platform build/check report for BioC 3.16:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:06:04 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for CytoTree on lconway


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? 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 470/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoTree 1.8.0  (landing page)
Yuting Dai
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/CytoTree
git_branch: RELEASE_3_16
git_last_commit: 1802ae8
git_last_commit_date: 2022-11-01 11:22:21 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  NO, package depends on 'flowUtils' which is not available
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'flowUtils' which is not available
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'flowUtils' which is not available

Summary

Package: CytoTree
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2023-04-10 19:43:55 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:49:02 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 306.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CytoTree.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/CytoTree.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.8.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'CytoTree' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.16-bioc/meat/CytoTree.Rcheck/00install.out’ for details.
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'as(<dsCMatrix>, "dsTMatrix")' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runCluster  10.671  0.041  10.725
plot2D       9.383  0.127   9.533
runMclust    7.042  0.025   7.089
plotCluster  5.990  0.036   6.044
runUMAP      5.043  0.089   5.142
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/CytoTree.Rcheck/00check.log’
for details.



Installation output

CytoTree.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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/4.2/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/4.2/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/4.2/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’
Warning: Package 'CytoTree' is deprecated and will be removed from Bioconductor
  version 3.17
** 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’
Warning: Package 'CytoTree' is deprecated and will be removed from Bioconductor
  version 3.17
** testing if installed package keeps a record of temporary installation path
* DONE (CytoTree)

Tests output


Example timings

CytoTree.Rcheck/CytoTree-Ex.timings

nameusersystemelapsed
CytoTree-package000
Rphenograph3.1980.0123.213
buildTree0.1050.0070.116
constraintMatrix0.0230.0000.024
correctBatchCYT1.6200.0051.627
createCYT0.0920.0130.114
defLeafCells0.0120.0010.014
defRootCells0.0160.0010.017
fetchCell0.0150.0010.017
fetchClustMeta0.0250.0020.028
fetchPlotMeta0.0230.0040.027
find_neighbors0.0010.0000.002
gatingMatrix0.0130.0010.015
plot2D9.3830.1279.533
plot3D0.0310.0030.034
plotBranchHeatmap0.2010.0070.209
plotCluster5.9900.0366.044
plotClusterHeatmap0.1950.0080.204
plotHeatmap0.4290.0240.456
plotMarkerDensity000
plotPieCluster2.7020.0612.769
plotPieTree0.2990.0090.308
plotPseudotimeDensity0.9010.0140.919
plotPseudotimeTraj3.7000.0523.758
plotTree1.3320.0131.349
plotViolin2.6790.0642.747
processingCluster0.3860.0230.409
runClara0.0360.0000.037
runCluster10.671 0.04110.725
runDiff0.0490.0010.050
runDiffusionMap0.1700.0190.189
runExprsExtract0.0100.0010.012
runExprsMerge0.0610.0040.065
runFastPCA0.0150.0010.016
runKmeans0.0130.0000.014
runMclust7.0420.0257.089
runPhenograph3.7630.0303.797
runPseudotime0.5930.0410.636
runSOM0.0230.0010.025
runTSNE2.5280.0582.593
runUMAP5.0430.0895.142
runWalk0.1150.0070.123
show-CYT-method0.0090.0000.009
subsetCYT0.0110.0000.012
updateClustMeta0.0170.0000.017
updatePlotMeta0.0100.0010.010