Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:30 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (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 |
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. |
Package 470/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Yuting Dai
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: CytoTree |
Version: 1.8.0 |
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CytoTree.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CytoTree_1.8.0.tar.gz |
StartedAt: 2023-04-11 00:34:28 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 00:40:23 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 355.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CytoTree.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CytoTree.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CytoTree_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CytoTree.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (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 whether package 'CytoTree' can be installed ... WARNING Found the following significant warnings: Warning: Package 'CytoTree' is deprecated and will be removed from Bioconductor See 'F:/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 for x64 is not available File 'F:/biocbuild/bbs-3.16-bioc/R/library/CytoTree/libs/x64/CytoTree.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 ... 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 12.39 0.00 12.39 plot2D 10.89 0.26 11.23 runMclust 8.31 0.00 8.32 plotCluster 6.78 0.11 6.89 runUMAP 5.59 0.09 5.69 plotPseudotimeTraj 5.14 0.05 5.19 * 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 'F:/biocbuild/bbs-3.16-bioc/meat/CytoTree.Rcheck/00check.log' for details.
CytoTree.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CytoTree ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'CytoTree' ... ** using staged installation ** libs g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c jaccard_coeff.cpp -o jaccard_coeff.o g++ -std=gnu++14 -shared -s -static-libgcc -o CytoTree.dll tmp.def RcppExports.o jaccard_coeff.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-CytoTree/00new/CytoTree/libs/x64 ** 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 ** 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)
CytoTree.Rcheck/CytoTree-Ex.timings
name | user | system | elapsed | |
CytoTree-package | 0 | 0 | 0 | |
Rphenograph | 3.45 | 0.00 | 3.50 | |
buildTree | 0.11 | 0.04 | 0.28 | |
constraintMatrix | 0.03 | 0.00 | 0.03 | |
correctBatchCYT | 0.95 | 0.00 | 1.06 | |
createCYT | 0.22 | 0.04 | 0.33 | |
defLeafCells | 0.02 | 0.00 | 0.02 | |
defRootCells | 0.01 | 0.00 | 0.01 | |
fetchCell | 0.02 | 0.00 | 0.02 | |
fetchClustMeta | 0.03 | 0.00 | 0.03 | |
fetchPlotMeta | 0.03 | 0.00 | 0.03 | |
find_neighbors | 0 | 0 | 0 | |
gatingMatrix | 0.02 | 0.00 | 0.02 | |
plot2D | 10.89 | 0.26 | 11.23 | |
plot3D | 0.05 | 0.00 | 0.06 | |
plotBranchHeatmap | 0.32 | 0.02 | 0.35 | |
plotCluster | 6.78 | 0.11 | 6.89 | |
plotClusterHeatmap | 0.32 | 0.00 | 0.31 | |
plotHeatmap | 0.48 | 0.04 | 0.53 | |
plotMarkerDensity | 0 | 0 | 0 | |
plotPieCluster | 2.98 | 0.10 | 3.08 | |
plotPieTree | 0.53 | 0.00 | 0.53 | |
plotPseudotimeDensity | 1.30 | 0.01 | 1.31 | |
plotPseudotimeTraj | 5.14 | 0.05 | 5.19 | |
plotTree | 2.59 | 0.03 | 2.63 | |
plotViolin | 2.80 | 0.06 | 2.86 | |
processingCluster | 0.61 | 0.00 | 0.67 | |
runClara | 0.03 | 0.00 | 0.04 | |
runCluster | 12.39 | 0.00 | 12.39 | |
runDiff | 0.05 | 0.00 | 0.04 | |
runDiffusionMap | 0.23 | 0.00 | 0.24 | |
runExprsExtract | 0.03 | 0.01 | 0.04 | |
runExprsMerge | 0.18 | 0.05 | 0.22 | |
runFastPCA | 0.01 | 0.00 | 0.02 | |
runKmeans | 0.02 | 0.00 | 0.01 | |
runMclust | 8.31 | 0.00 | 8.32 | |
runPhenograph | 4.02 | 0.00 | 4.02 | |
runPseudotime | 0.62 | 0.03 | 0.65 | |
runSOM | 0.03 | 0.00 | 0.04 | |
runTSNE | 2.91 | 0.03 | 2.93 | |
runUMAP | 5.59 | 0.09 | 5.69 | |
runWalk | 0.14 | 0.00 | 0.14 | |
show-CYT-method | 0.02 | 0.00 | 0.02 | |
subsetCYT | 0.01 | 0.00 | 0.01 | |
updateClustMeta | 0.02 | 0.00 | 0.02 | |
updatePlotMeta | 0.02 | 0.00 | 0.01 | |