Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:05:02 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 nebbiolo2


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: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
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 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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  UNNEEDED, same version is already published

Summary

Package: CytoTree
Version: 1.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CytoTree.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CytoTree_1.4.0.tar.gz
StartedAt: 2022-01-20 06:59:37 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 07:06:17 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 399.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoTree.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CytoTree.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CytoTree_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CytoTree.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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    12.932  0.012  12.945
plot2D         8.508  0.236   8.744
runMclust      7.512  0.004   7.516
Rphenograph    5.098  0.316   5.414
plotCluster    5.333  0.012   5.346
runUMAP        5.217  0.016   5.234
runPhenograph  5.079  0.004   5.083
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/CytoTree.Rcheck/00check.log’
for details.



Installation output

CytoTree.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CytoTree
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘CytoTree’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c jaccard_coeff.cpp -o jaccard_coeff.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o CytoTree.so RcppExports.o jaccard_coeff.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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-package000
Rphenograph5.0980.3165.414
buildTree0.1310.0000.132
constraintMatrix0.0260.0000.027
correctBatchCYT2.5320.0162.561
createCYT0.1070.0000.130
defLeafCells0.0160.0000.016
defRootCells0.0160.0000.016
fetchCell0.0170.0000.017
fetchClustMeta0.0240.0040.028
fetchPlotMeta0.030.000.03
find_neighbors0.0020.0000.001
gatingMatrix0.0180.0000.018
plot2D8.5080.2368.744
plot3D0.0380.0040.043
plotBranchHeatmap0.1890.0080.197
plotCluster5.3330.0125.346
plotClusterHeatmap0.2030.0080.211
plotHeatmap0.4960.0120.507
plotMarkerDensity000
plotPieCluster3.3250.0283.353
plotPieTree0.4560.0040.459
plotPseudotimeDensity0.9210.0000.921
plotPseudotimeTraj4.2780.0364.314
plotTree1.2430.0001.243
plotViolin3.9440.1044.048
processingCluster0.4070.0000.407
runClara0.0810.0000.081
runCluster12.932 0.01212.945
runDiff0.0590.0000.059
runDiffusionMap0.2330.0360.269
runExprsExtract0.0090.0000.009
runExprsMerge0.0460.0000.046
runFastPCA0.0150.0000.015
runKmeans0.0150.0000.015
runMclust7.5120.0047.516
runPhenograph5.0790.0045.083
runPseudotime1.4710.0241.495
runSOM0.0280.0000.028
runTSNE3.3570.0163.374
runUMAP5.2170.0165.234
runWalk0.2280.0000.228
show-CYT-method0.0120.0000.012
subsetCYT0.0150.0000.014
updateClustMeta0.0220.0000.023
updatePlotMeta0.0140.0000.013