Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:24 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the sva package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sva.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 1876/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sva 3.40.0 (landing page) Jeffrey T. Leek
| 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: sva |
Version: 3.40.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sva.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sva_3.40.0.tar.gz |
StartedAt: 2021-10-15 06:21:19 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 06:27:23 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 364.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sva.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sva.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sva_3.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/sva.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'sva/DESCRIPTION' ... OK * this is package 'sva' version '3.40.0' * 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 'sva' 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 ... OK * 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 sva_network 8.89 0.28 9.17 sva.check 6.13 0.42 6.54 read.degradation.matrix 1.44 0.05 6.63 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sva_network 9.83 0.27 10.10 sva.check 6.20 0.36 6.56 read.degradation.matrix 1.41 0.00 5.81 * 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: OK
sva.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/sva_3.40.0.tar.gz && rm -rf sva.buildbin-libdir && mkdir sva.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sva.buildbin-libdir sva_3.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sva_3.40.0.zip && rm sva_3.40.0.tar.gz sva_3.40.0.zip ### ############################################################################## ############################################################################## % 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 203k 100 203k 0 0 888k 0 --:--:-- --:--:-- --:--:-- 891k install for i386 * installing *source* package 'sva' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sva.c -o sva.o sva.c:27:34: warning: missing braces around initializer [-Wmissing-braces] R_CallMethodDef callMethods[] = { ^ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/sva.buildbin-libdir/00LOCK-sva/00new/sva/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'sva' finding HTML links ... done ComBat html ComBat_seq html empirical.controls html f.pvalue html fstats html fsva html irwsva.build html num.sv html psva html qsva html read.degradation.matrix html ssva html sva html sva.check html sva_network html svaseq html twostepsva.build 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 'sva' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sva.c -o sva.o sva.c:27:34: warning: missing braces around initializer [-Wmissing-braces] R_CallMethodDef callMethods[] = { ^ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/sva.buildbin-libdir/sva/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'sva' as sva_3.40.0.zip * DONE (sva) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'sva' successfully unpacked and MD5 sums checked
sva.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > library(testthat) > library(sva) Loading required package: mgcv Loading required package: nlme This is mgcv 1.8-38. For overview type 'help("mgcv-package")'. Loading required package: genefilter Loading required package: BiocParallel > > test_check("sva") Found 2 batches Using full model in ComBat-seq. Adjusting for 1 covariate(s) or covariate level(s) [ FAIL 0 | WARN 1 | SKIP 0 | PASS 33 ] > > proc.time() user system elapsed 48.70 1.82 50.51 |
sva.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > library(testthat) > library(sva) Loading required package: mgcv Loading required package: nlme This is mgcv 1.8-38. For overview type 'help("mgcv-package")'. Loading required package: genefilter Loading required package: BiocParallel > > test_check("sva") Found 2 batches Using full model in ComBat-seq. Adjusting for 1 covariate(s) or covariate level(s) [ FAIL 0 | WARN 1 | SKIP 0 | PASS 33 ] > > proc.time() user system elapsed 53.57 1.31 54.87 |
sva.Rcheck/examples_i386/sva-Ex.timings
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sva.Rcheck/examples_x64/sva-Ex.timings
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