Joshua Campbell
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/celda |
| Branch: RELEASE_3_9 |
| Last Commit: e2cf9f9 |
| Last Changed Date: 2019-06-03 13:53:29 -0400 (Mon, 03 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:44:21 -0400 (Wed, 16 Oct 2019).
| Package 224/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| celda 1.0.4 Joshua Campbell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: celda |
| Version: 1.0.4 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:celda.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings celda_1.0.4.tar.gz |
| StartedAt: 2019-10-16 02:29:31 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:41:41 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 730.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: celda.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:celda.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings celda_1.0.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/celda.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'celda/DESCRIPTION' ... OK
* this is package 'celda' version '1.0.4'
* 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 'celda' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.9-bioc/R/library/celda/libs/i386/celda.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-3.9-bioc/R/library/celda/libs/x64/celda.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 or elapsed time > 5s
user system elapsed
geneSetEnrich 14.98 0.17 15.15
recursiveSplitCell 11.62 0.20 11.83
recursiveSplitModule 7.72 0.52 8.23
plotDimReduceGrid 7.99 0.18 8.16
celda_CG 6.35 0.12 6.47
celdaCGMod 6.32 0.05 6.36
celdaTsne-celda_CG-method 5.01 0.10 5.20
celdaCGGridSearchRes 1.31 0.11 46.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneSetEnrich 17.39 0.13 17.52
plotDimReduceGrid 8.61 0.03 8.64
recursiveSplitCell 8.38 0.00 8.38
celdaCGMod 6.34 0.07 6.40
recursiveSplitModule 5.86 0.02 5.88
celda_CG 5.86 0.00 5.86
celdaCGGridSearchRes 0.67 0.03 46.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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-3.9-bioc/meat/celda.Rcheck/00check.log'
for details.
celda.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/celda_1.0.4.tar.gz && rm -rf celda.buildbin-libdir && mkdir celda.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=celda.buildbin-libdir celda_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL celda_1.0.4.zip && rm celda_1.0.4.tar.gz celda_1.0.4.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'celda' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c eigenMatMultInt.cpp -o eigenMatMultInt.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c matrixNorm.cpp -o matrixNorm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c matrixSums.c -o matrixSums.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c perplexity.c -o perplexity.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o celda.dll tmp.def RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o perplexity.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/celda.buildbin-libdir/00LOCK-celda/00new/celda/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'celda'
finding HTML links ... done
appendCeldaList html
availableModels html
bestLogLikelihood-celdaModel-method html
bestLogLikelihood html
celda html
celdaCGGridSearchRes html
celdaCGMod html
celdaCGSim html
celdaCMod html
celdaCSim html
celdaGMod html
celdaGSim html
celdaGridSearch html
celdaHeatmap-celda_C-method html
celdaHeatmap-celda_CG-method html
celdaHeatmap-celda_G-method html
celdaHeatmap html
celdaPerplexity-celdaList-method html
celdaPerplexity html
celdaProbabilityMap-celda_C-method html
celdaProbabilityMap-celda_CG-method html
celdaProbabilityMap html
celdaTsne-celda_C-method html
celdaTsne-celda_CG-method html
celdaTsne-celda_G-method html
celdaTsne html
celdaUmap-celda_C-method html
celdaUmap-celda_CG-method html
celdaUmap-celda_G-method html
celdaUmap html
celda_C html
celda_CG html
celda_G html
clusterProbability-celda_C-method html
clusterProbability-celda_CG-method html
clusterProbability-celda_G-method html
clusterProbability html
clusters-celdaModel-method html
clusters html
compareCountMatrix html
contaminationSim html
countChecksum-celdaList-method html
countChecksum html
decontX html
differentialExpression html
distinctColors html
eigenMatMultInt html
factorizeMatrix-celda_C-method html
factorizeMatrix-celda_CG-method html
factorizeMatrix-celda_G-method html
factorizeMatrix html
fastNormProp html
fastNormPropLog html
fastNormPropSqrt html
featureModuleLookup-celda_C-method html
featureModuleLookup-celda_CG-method html
featureModuleLookup-celda_G-method html
featureModuleLookup html
featureModuleTable html
geneSetEnrich html
logLikelihood html
logLikelihoodHistory-celdaModel-method
html
logLikelihoodHistory html
logLikelihoodcelda_C html
logLikelihoodcelda_CG html
logLikelihoodcelda_G html
matrixNames-celdaModel-method html
matrixNames html
moduleHeatmap html
normalizeCounts html
params-celdaModel-method html
params html
perplexity-celda_C-method html
perplexity-celda_CG-method html
perplexity-celda_G-method html
perplexity html
plotDimReduceCluster html
plotDimReduceFeature html
plotDimReduceGrid html
plotDimReduceModule html
plotGridSearchPerplexity html
plotGridSearchPerplexitycelda_C html
plotGridSearchPerplexitycelda_CG html
plotGridSearchPerplexitycelda_G html
plotHeatmap html
recodeClusterY html
recodeClusterZ html
recursiveSplitCell html
recursiveSplitModule html
resList-celdaList-method html
resList html
resamplePerplexity html
runParams-celdaList-method html
runParams html
sampleCells html
sampleLabel-celdaModel-method html
sampleLabel html
selectBestModel html
semiPheatmap html
simulateCells html
simulateCellscelda_C html
simulateCellscelda_CG html
simulateCellscelda_G html
simulateContaminatedMatrix html
subsetCeldaList html
topRank html
violinPlot html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'celda' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c eigenMatMultInt.cpp -o eigenMatMultInt.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c matrixNorm.cpp -o matrixNorm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c matrixSums.c -o matrixSums.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c perplexity.c -o perplexity.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o celda.dll tmp.def RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o perplexity.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/celda.buildbin-libdir/celda/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'celda' as celda_1.0.4.zip
* DONE (celda)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'celda' successfully unpacked and MD5 sums checked
|
celda.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("celda")
Loading required package: celda
== testthat results ===========================================================
[ OK: 232 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
60.04 3.76 64.48
|
celda.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("celda")
Loading required package: celda
== testthat results ===========================================================
[ OK: 232 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
67.00 1.00 69.45
|
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celda.Rcheck/examples_i386/celda-Ex.timings
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celda.Rcheck/examples_x64/celda-Ex.timings
|