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CHECK report for sva on merida1

This page was generated on 2019-04-16 11:56:08 -0400 (Tue, 16 Apr 2019).

Package 1529/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sva 3.30.1
Jeffrey T. Leek , John D. Storey
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/sva
Branch: RELEASE_3_8
Last Commit: fdb98bc
Last Changed Date: 2019-01-04 13:12:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: sva
Version: 3.30.1
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_3.30.1.tar.gz
StartedAt: 2019-04-16 03:03:03 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:06:12 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 188.8 seconds
RetCode: 0
Status:  OK 
CheckDir: sva.Rcheck
Warnings: 0

Command output

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###
### 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_3.30.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/sva.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sva/DESCRIPTION’ ... OK
* this is package ‘sva’ version ‘3.30.1’
* 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 ... NOTE
sva_network: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
sva.check   7.730  0.403   8.203
sva_network 5.895  0.277   6.213
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/sva.Rcheck/00check.log’
for details.



Installation output

sva.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sva
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘sva’ ...
** libs
clang -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
  ^˜˜˜
  {   }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -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/3.5/Resources/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)

Tests output

sva.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 1.8-28. 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 
 25.216   8.205  31.493 

Example timings

sva.Rcheck/sva-Ex.timings

nameusersystemelapsed
ComBat0.9290.0390.974
empirical.controls2.0040.0892.100
f.pvalue0.2610.0160.277
fstats0.2620.0200.283
fsva0.5030.0270.539
irwsva.build1.2950.0621.364
num.sv0.9670.0491.024
psva0.4680.0180.490
qsva0.5970.2590.724
read.degradation.matrix1.2690.5650.891
ssva0.8270.0780.911
sva1.5290.0911.627
sva.check7.7300.4038.203
sva_network5.8950.2776.213
svaseq0.8250.1120.954
twostepsva.build4.0680.2744.388