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CHECK report for sva on tokay2

This page was generated on 2018-10-17 08:35:49 -0400 (Wed, 17 Oct 2018).

Package 1450/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sva 3.28.0
Jeffrey T. Leek , John D. Storey
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/sva
Branch: RELEASE_3_7
Last Commit: dd49372
Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sva
Version: 3.28.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sva.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings sva_3.28.0.tar.gz
StartedAt: 2018-10-17 05:06:39 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:10:28 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 229.6 seconds
RetCode: 0
Status:  OK  
CheckDir: sva.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sva.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings sva_3.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/sva.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
read.degradation.matrix 0.61   0.02    5.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
sva.check 4.87   0.42    5.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/sva_3.28.0.tar.gz && rm -rf sva.buildbin-libdir && mkdir sva.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sva.buildbin-libdir sva_3.28.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL sva_3.28.0.zip && rm sva_3.28.0.tar.gz sva_3.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  199k  100  199k    0     0  3169k      0 --:--:-- --:--:-- --:--:-- 3619k

install for i386

* installing *source* package 'sva' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sva.c -o sva.o
sva.c:30:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
sva.c:30:1: warning: (near initialization for 'callMethods[1]') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/sva.buildbin-libdir/sva/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sva'
    finding HTML links ... done
    ComBat                                  html  
    empirical.controls                      html  
    f.pvalue                                html  
    fstats                                  html  
    fsva                                    html  
    irwsva.build                            html  
    num.sv                                  html  
    psva                                    html  
    qsva                                    html  
    read.degradation.matrix                 html  
    ssva                                    html  
    sva                                     html  
    sva.check                               html  
    svaseq                                  html  
    twostepsva.build                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sva' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sva.c -o sva.o
sva.c:30:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
sva.c:30:1: warning: (near initialization for 'callMethods[1]') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/sva.buildbin-libdir/sva/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sva' as sva_3.28.0.zip
* DONE (sva)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'sva' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

sva.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 31 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  18.85    1.14   19.98

sva.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 1.8-24. 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: 31 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  20.40    1.26   21.67

Example timings

sva.Rcheck/examples_i386/sva-Ex.timings

nameusersystemelapsed
ComBat0.390.050.44
empirical.controls1.810.061.88
f.pvalue0.290.000.28
fstats0.250.030.28
fsva0.370.030.41
irwsva.build1.330.081.41
num.sv0.500.050.54
psva0.620.000.63
qsva0.380.073.11
read.degradation.matrix0.610.025.64
ssva0.800.060.86
sva0.790.060.86
sva.check0.530.040.57
svaseq0.860.040.90
twostepsva.build2.950.143.10

sva.Rcheck/examples_x64/sva-Ex.timings

nameusersystemelapsed
ComBat0.830.030.86
empirical.controls1.590.191.78
f.pvalue0.250.000.25
fstats0.200.030.24
fsva0.360.030.39
irwsva.build0.880.121.00
num.sv0.820.020.84
psva0.330.030.36
qsva0.280.022.02
read.degradation.matrix0.320.033.76
ssva0.750.030.78
sva1.560.111.68
sva.check4.870.425.29
svaseq0.550.010.57
twostepsva.build3.110.083.18