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This page was generated on 2025-08-21 11:42 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2136/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sva 3.56.0  (landing page)
Jeffrey T. Leek , John D. Storey
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/sva
git_branch: RELEASE_3_21
git_last_commit: b128ddd
git_last_commit_date: 2025-04-15 10:11:05 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sva on kunpeng2

To the developers/maintainers of the sva package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: sva
Version: 3.56.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:sva.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sva_3.56.0.tar.gz
StartedAt: 2025-08-19 14:44:36 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 14:49:37 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 300.4 seconds
RetCode: 0
Status:   OK  
CheckDir: sva.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sva.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sva_3.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sva.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sva/DESCRIPTION’ ... OK
* this is package ‘sva’ version ‘3.56.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘sva’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
sva_network      13.073  0.231  13.333
twostepsva.build 12.008  0.084  12.110
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sva
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘sva’ ...
** this is package ‘sva’ version ‘3.56.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c sva.c -o sva.o
sva.c:27:34: warning: missing braces around initializer [-Wmissing-braces]
   27 | R_CallMethodDef callMethods[]  = {
      |                                  ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o sva.so sva.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-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)

Tests output

sva.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 1.9-3. 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 
 86.723   4.030  89.118 

Example timings

sva.Rcheck/sva-Ex.timings

nameusersystemelapsed
ComBat3.3020.1003.408
ComBat_seq0.2000.0040.204
empirical.controls3.0740.1123.192
f.pvalue0.2970.0180.315
fstats0.2930.0080.302
fsva0.4930.0160.509
irwsva.build2.5110.0152.532
num.sv1.5290.0641.595
psva0.4400.0040.445
qsva0.4330.2330.560
read.degradation.matrix0.7360.4880.569
ssva0.9330.0881.023
sva0.9930.0281.022
sva.check1.5570.2161.776
sva_network13.073 0.23113.333
svaseq0.8900.0160.909
twostepsva.build12.008 0.08412.110