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) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
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 | |