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This page was generated on 2021-10-21 12:05:35 -0400 (Thu, 21 Oct 2021).

CHECK results for sva on merida1

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.

raw results

Package 1902/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sva 3.41.0  (landing page)
Jeffrey T. Leek , John D. Storey
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/sva
git_branch: master
git_last_commit: 43373e4
git_last_commit_date: 2021-05-19 11:50:23 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: sva
Version: 3.41.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sva.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sva_3.41.0.tar.gz
StartedAt: 2021-10-21 09:54:19 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 09:59:35 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 316.4 seconds
RetCode: 0
Status:   OK  
CheckDir: sva.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sva.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sva_3.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/sva.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘3.41.0’
* 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
* 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 13.928  0.314  14.266
sva.check    8.142  0.485   8.637
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sva
###
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* 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/11.0.0/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)

Tests output

sva.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "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 
 87.632   6.093  91.149 

Example timings

sva.Rcheck/sva-Ex.timings

nameusersystemelapsed
ComBat2.1950.0732.275
ComBat_seq0.2260.0050.231
empirical.controls2.0320.1102.144
f.pvalue0.3550.0190.374
fstats0.3220.0150.337
fsva0.5900.0320.624
irwsva.build1.4930.0721.567
num.sv0.8040.0300.834
psva0.9680.0280.998
qsva0.6720.4020.734
read.degradation.matrix1.3670.7830.915
ssva0.8560.0580.915
sva1.4670.0901.557
sva.check8.1420.4858.637
sva_network13.928 0.31414.266
svaseq0.8080.0280.840
twostepsva.build4.1750.1324.315