Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for sva on palomino5


To the developers/maintainers of the sva package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1980/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sva 3.47.0  (landing page)
Jeffrey T. Leek , John D. Storey
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/sva
git_branch: master
git_last_commit: c9e092f
git_last_commit_date: 2022-11-01 11:06:24 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: sva
Version: 3.47.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sva.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sva_3.47.0.tar.gz
StartedAt: 2022-12-29 04:03:29 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:06:33 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 183.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sva.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sva.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sva_3.47.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/sva.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sva/DESCRIPTION' ... OK
* this is package 'sva' version '3.47.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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    8   0.25    8.25
* 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: OK


Installation output

sva.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL sva
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'sva' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/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]
   27 | R_CallMethodDef callMethods[]  = {
      |                                  ^
gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-sva/00new/sva/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sva)

Tests output

sva.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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 1.8-41. 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 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  37.98    2.17   40.14 

Example timings

sva.Rcheck/sva-Ex.timings

nameusersystemelapsed
ComBat1.400.051.61
ComBat_seq0.130.000.13
empirical.controls0.970.061.04
f.pvalue0.190.000.18
fstats0.530.000.53
fsva0.230.070.35
irwsva.build0.940.061.00
num.sv0.440.010.46
psva0.570.030.61
qsva0.690.102.15
read.degradation.matrix0.970.084.07
ssva0.480.010.50
sva1.270.031.29
sva.check0.900.050.95
sva_network8.000.258.25
svaseq0.450.060.64
twostepsva.build2.650.102.74