Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:55 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sva.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sva_3.40.0.tar.gz |
StartedAt: 2021-10-15 00:32:07 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:37:08 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 300.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sva.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sva.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sva_3.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/sva.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... 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 * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sva_network 14.266 0.366 14.648 sva.check 7.721 0.435 8.197 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/sva.Rcheck/00check.log’ for details.
sva.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sva ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘sva’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sva.c -o sva.o sva.c:29:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] NULL ^~~~ { } /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include/stddef.h:105:16: note: expanded from macro 'NULL' # define NULL ((void*)0) ^~~~~~~~~~ 1 warning generated. clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sva.so sva.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-sva/00new/sva/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sva)
sva.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0 | SKIP 0 | PASS 33 ] > > proc.time() user system elapsed 85.599 4.964 89.227
sva.Rcheck/sva-Ex.timings
name | user | system | elapsed | |
ComBat | 2.576 | 0.038 | 2.621 | |
ComBat_seq | 0.255 | 0.003 | 0.258 | |
empirical.controls | 1.692 | 0.106 | 1.803 | |
f.pvalue | 0.367 | 0.025 | 0.393 | |
fstats | 0.314 | 0.010 | 0.324 | |
fsva | 0.949 | 0.025 | 0.977 | |
irwsva.build | 1.404 | 0.052 | 1.458 | |
num.sv | 0.632 | 0.020 | 0.652 | |
psva | 0.453 | 0.016 | 0.470 | |
qsva | 0.631 | 0.384 | 0.656 | |
read.degradation.matrix | 1.299 | 0.680 | 0.863 | |
ssva | 1.338 | 0.147 | 1.486 | |
sva | 1.585 | 0.098 | 1.683 | |
sva.check | 7.721 | 0.435 | 8.197 | |
sva_network | 14.266 | 0.366 | 14.648 | |
svaseq | 0.833 | 0.029 | 0.862 | |
twostepsva.build | 4.080 | 0.149 | 4.235 | |