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This page was generated on 2021-10-22 12:04:46 -0400 (Fri, 22 Oct 2021).

CHECK results for sva on riesling1

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
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raw results

Package 1902/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sva 3.41.0  (landing page)
Jeffrey T. Leek , John D. Storey
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 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: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sva.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sva_3.41.0.tar.gz
StartedAt: 2021-10-22 03:30:00 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 03:35:48 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 347.4 seconds
RetCode: 0
Status:   OK  
CheckDir: sva.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sva.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sva_3.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/sva.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '3.41.0'
* 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 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 (user + system) or elapsed time > 5s
            user system elapsed
sva_network 6.64   0.22    6.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
sva_network 7.08   0.17    7.25
sva.check   5.22   0.22    5.44
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/sva_3.41.0.tar.gz && rm -rf sva.buildbin-libdir && mkdir sva.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sva.buildbin-libdir sva_3.41.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL sva_3.41.0.zip && rm sva_3.41.0.tar.gz sva_3.41.0.zip
###
##############################################################################
##############################################################################


  % 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  203k  100  203k    0     0   904k      0 --:--:-- --:--:-- --:--:--  904k

install for i386

* installing *source* package 'sva' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sva.c -o sva.o
sva.c:27:34: warning: missing braces around initializer [-Wmissing-braces]
 R_CallMethodDef callMethods[]  = {
                                  ^
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/sva.buildbin-libdir/00LOCK-sva/00new/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  
    ComBat_seq                              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  
    sva_network                             html  
    svaseq                                  html  
    twostepsva.build                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'sva' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sva.c -o sva.o
sva.c:27:34: warning: missing braces around initializer [-Wmissing-braces]
 R_CallMethodDef callMethods[]  = {
                                  ^
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/sva.buildbin-libdir/sva/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sva' as sva_3.41.0.zip
* DONE (sva)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'sva' successfully unpacked and MD5 sums checked

Tests output

sva.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 1.8-38. 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 1 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  37.21    0.64   37.85 

sva.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 1.8-38. 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 1 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  35.37    0.90   36.26 

Example timings

sva.Rcheck/examples_i386/sva-Ex.timings

nameusersystemelapsed
ComBat0.750.000.75
ComBat_seq0.160.000.16
empirical.controls1.460.051.50
f.pvalue0.170.010.18
fstats0.190.000.19
fsva0.290.000.30
irwsva.build1.140.031.17
num.sv0.640.030.67
psva0.280.000.28
qsva0.480.031.64
read.degradation.matrix0.800.023.75
ssva0.390.030.42
sva0.800.100.89
sva.check4.420.294.72
sva_network6.640.226.86
svaseq0.420.050.47
twostepsva.build2.270.042.31

sva.Rcheck/examples_x64/sva-Ex.timings

nameusersystemelapsed
ComBat1.060.021.08
ComBat_seq0.110.000.11
empirical.controls1.200.051.25
f.pvalue0.190.000.18
fstats0.170.000.18
fsva0.300.010.31
irwsva.build0.790.070.86
num.sv0.390.030.43
psva0.300.050.34
qsva0.610.011.66
read.degradation.matrix1.000.023.23
ssva0.520.000.52
sva1.150.031.18
sva.check5.220.225.44
sva_network7.080.177.25
svaseq0.370.060.44
twostepsva.build2.360.132.48