Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).
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. |
Package 436/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CytoTree 1.2.0 (landing page) Yuting Dai
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: CytoTree |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CytoTree.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CytoTree_1.2.0.tar.gz |
StartedAt: 2021-10-14 09:27:59 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:33:19 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 320.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CytoTree.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CytoTree.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CytoTree_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CytoTree.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.2.0’ * 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 11.855 0.020 11.876 plot2D 7.863 0.124 7.987 runMclust 7.402 0.004 7.407 runUMAP 5.019 0.047 5.068 * 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-3.13-bioc/meat/CytoTree.Rcheck/00check.log’ for details.
CytoTree.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CytoTree ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘CytoTree’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -L/usr/local/lib -o CytoTree.so RcppExports.o jaccard_coeff.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-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)
CytoTree.Rcheck/CytoTree-Ex.timings
name | user | system | elapsed | |
CytoTree-package | 0 | 0 | 0 | |
Rphenograph | 4.087 | 0.016 | 4.103 | |
buildTree | 0.114 | 0.004 | 0.120 | |
constraintMatrix | 0.024 | 0.000 | 0.024 | |
correctBatchCYT | 2.079 | 0.023 | 2.096 | |
createCYT | 0.080 | 0.002 | 0.083 | |
defLeafCells | 0.016 | 0.000 | 0.015 | |
defRootCells | 0.015 | 0.000 | 0.015 | |
fetchCell | 0.016 | 0.000 | 0.016 | |
fetchClustMeta | 0.027 | 0.000 | 0.026 | |
fetchPlotMeta | 0.023 | 0.007 | 0.030 | |
find_neighbors | 0.001 | 0.001 | 0.002 | |
gatingMatrix | 0.015 | 0.000 | 0.016 | |
plot2D | 7.863 | 0.124 | 7.987 | |
plot3D | 0.04 | 0.00 | 0.04 | |
plotBranchHeatmap | 0.194 | 0.000 | 0.194 | |
plotCluster | 4.564 | 0.012 | 4.576 | |
plotClusterHeatmap | 0.185 | 0.004 | 0.189 | |
plotHeatmap | 0.448 | 0.019 | 0.468 | |
plotMarkerDensity | 0 | 0 | 0 | |
plotPieCluster | 3.113 | 0.025 | 3.138 | |
plotPieTree | 0.443 | 0.000 | 0.443 | |
plotPseudotimeDensity | 0.771 | 0.000 | 0.771 | |
plotPseudotimeTraj | 3.872 | 0.016 | 3.888 | |
plotTree | 1.164 | 0.004 | 1.168 | |
plotViolin | 3.477 | 0.027 | 3.506 | |
processingCluster | 0.374 | 0.007 | 0.381 | |
runClara | 0.038 | 0.004 | 0.042 | |
runCluster | 11.855 | 0.020 | 11.876 | |
runDiff | 0.048 | 0.004 | 0.052 | |
runDiffusionMap | 0.219 | 0.012 | 0.232 | |
runExprsExtract | 0.008 | 0.000 | 0.009 | |
runExprsMerge | 0.038 | 0.003 | 0.042 | |
runFastPCA | 0.015 | 0.001 | 0.015 | |
runKmeans | 0.014 | 0.000 | 0.014 | |
runMclust | 7.402 | 0.004 | 7.407 | |
runPhenograph | 4.384 | 0.016 | 4.400 | |
runPseudotime | 0.564 | 0.004 | 0.568 | |
runSOM | 0.027 | 0.000 | 0.027 | |
runTSNE | 3.293 | 0.000 | 3.293 | |
runUMAP | 5.019 | 0.047 | 5.068 | |
runWalk | 0.215 | 0.004 | 0.218 | |
show-CYT-method | 0.013 | 0.001 | 0.013 | |
subsetCYT | 0.016 | 0.000 | 0.016 | |
updateClustMeta | 0.024 | 0.000 | 0.024 | |
updatePlotMeta | 0.014 | 0.000 | 0.014 | |