Package: sva

Version: 3.28.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:sva.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings sva_3.28.0.tar.gz

StartedAt: 2018-10-16 04:04:22 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 04:06:20 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 118.0 seconds

RetCode: 0

Status:  OK

CheckDir: sva.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:sva.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings sva_3.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/sva.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sva/DESCRIPTION’ ... OK
* this is package ‘sva’ version ‘3.28.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
sva.check 5.104  0.048   5.155
* 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

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL sva
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘sva’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sva.c -o sva.o
sva.c:27:34: warning: missing braces around initializer [-Wmissing-braces]
 R_CallMethodDef callMethods[]  = {
                                  ^
sva.c:27:34: note: (near initialization for ‘callMethods’)
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o sva.so sva.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (sva)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1.8-24. For overview type 'help("mgcv-package")'.
Loading required package: genefilter
Loading required package: BiocParallel
> 
> test_check("sva")
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Using batch = 1 as a reference batch (this batch won't change)
Standardizing Data across genes
Using batch = 3 as a reference batch (this batch won't change)
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Using batch = 1 as a reference batch (this batch won't change)
Standardizing Data across genes
Using batch = 3 as a reference batch (this batch won't change)
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Using batch = 1 as a reference batch (this batch won't change)
Standardizing Data across genes
Using batch = 2 as a reference batch (this batch won't change)
Standardizing Data across genes
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 30 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 18.284   2.512  19.546 

name	user	system	elapsed
ComBat	0.812	0.132	0.965
empirical.controls	1.724	0.020	1.746
f.pvalue	0.240	0.000	0.242
fstats	0.232	0.004	0.236
fsva	0.400	0.008	0.418
irwsva.build	1.036	0.012	1.048
num.sv	0.764	0.000	0.763
psva	0.34	0.00	0.34
qsva	0.300	0.152	0.451
read.degradation.matrix	0.776	0.400	0.755
ssva	0.636	0.036	0.673
sva	1.084	0.004	1.092
sva.check	5.104	0.048	5.155
svaseq	0.548	0.004	0.553
twostepsva.build	3.024	0.008	3.030