Yuting Dai
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/CytoTree |
| Branch: RELEASE_3_12 |
| Last Commit: 929282c |
| Last Changed Date: 2020-11-08 07:16:03 -0400 (Sun, 08 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:35 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the CytoTree package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 419/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoTree 1.0.3 (landing page) Yuting Dai
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CytoTree |
| Version: 1.0.3 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CytoTree_1.0.3.tar.gz |
| StartedAt: 2021-05-06 01:57:15 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:07:11 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 595.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoTree.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CytoTree_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CytoTree.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CytoTree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoTree' version '1.0.3'
* 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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CytoTree/libs/i386/CytoTree.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CytoTree/libs/x64/CytoTree.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runCluster 15.70 0.01 15.71
runMclust 11.01 0.00 11.01
plot2D 10.27 0.51 10.78
runUMAP 5.98 0.11 6.10
plotCluster 5.23 0.00 5.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runCluster 14.25 0.02 14.26
plot2D 12.47 0.15 12.63
runMclust 10.17 0.00 10.17
plotCluster 6.44 0.02 6.46
runUMAP 5.63 0.01 5.65
plotPseudotimeTraj 5.62 0.00 5.63
* 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/CytoTree.Rcheck/00check.log'
for details.
CytoTree.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CytoTree_1.0.3.tar.gz && rm -rf CytoTree.buildbin-libdir && mkdir CytoTree.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoTree.buildbin-libdir CytoTree_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CytoTree_1.0.3.zip && rm CytoTree_1.0.3.tar.gz CytoTree_1.0.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1598k 100 1598k 0 0 13.2M 0 --:--:-- --:--:-- --:--:-- 13.3M
install for i386
* installing *source* package 'CytoTree' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CytoTree.dll tmp.def RcppExports.o jaccard_coeff.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CytoTree.buildbin-libdir/00LOCK-CytoTree/00new/CytoTree/libs/i386
** 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
converting help for package 'CytoTree'
finding HTML links ... done
CYT-class html
CytoTree-package html
Rphenograph html
addMetaData html
buildTree html
changeMarker html
constraintMatrix html
correctBatchCYT html
createCYT html
defLeafCells html
defRootCells html
fetchCell html
fetchClustMeta html
fetchPlotMeta html
find_neighbors html
gatingMatrix html
plot2D html
plot3D html
plotBranchHeatmap html
plotCluster html
plotClusterHeatmap html
plotHeatmap html
plotMarkerDensity html
plotPieCluster html
plotPieTree html
plotPseudotimeDensity html
plotPseudotimeTraj html
plotTrajHeatmap html
plotTree html
plotViolin html
processingCluster html
runClara html
runCluster html
runDiff html
runDiffusionMap html
runExprsExtract html
runExprsMerge html
runFastPCA html
runHclust html
runKNN html
runKmeans html
runMclust html
runPhenograph html
runPseudotime html
runSOM html
finding level-2 HTML links ... done
runTSNE html
runUMAP html
runWalk html
show-CYT-method html
subsetCYT html
updateClustMeta html
updatePlotMeta html
** 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'
** 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
install for x64
* installing *source* package 'CytoTree' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CytoTree.dll tmp.def RcppExports.o jaccard_coeff.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CytoTree.buildbin-libdir/CytoTree/libs/x64
** testing if installed package can be loaded
No methods found in package 'flowCore' for requests: 'action', 'assign', 'Data', 'gate', 'tree' when loading 'flowUtils'
* MD5 sums
packaged installation of 'CytoTree' as CytoTree_1.0.3.zip
* DONE (CytoTree)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CytoTree' successfully unpacked and MD5 sums checked
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CytoTree.Rcheck/examples_i386/CytoTree-Ex.timings
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CytoTree.Rcheck/examples_x64/CytoTree-Ex.timings
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