Back to "Blame Jeroen" build/check report for BioC 3.11

CHECK report for vsn on tokay2

This page was generated on 2020-04-14 03:20:16 -0400 (Tue, 14 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE vsn PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 86/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vsn 3.55.0
Wolfgang Huber
Snapshot Date: 2020-04-13 17:00:10 -0400 (Mon, 13 Apr 2020)
URL: https://git.bioconductor.org/packages/vsn
Branch: master
Last Commit: dcd6013
Last Changed Date: 2019-10-29 13:34:31 -0400 (Tue, 29 Oct 2019)
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK 

Summary

Package: vsn
Version: 3.55.0
Command: C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:vsn.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings vsn_3.55.0.tar.gz
StartedAt: 2020-04-13 22:51:50 -0400 (Mon, 13 Apr 2020)
EndedAt: 2020-04-13 22:53:30 -0400 (Mon, 13 Apr 2020)
EllapsedTime: 99.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: vsn.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:vsn.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings vsn_3.55.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/vsn.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'vsn/DESCRIPTION' ... OK
* this is package 'vsn' version '3.55.0'
* 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 'vsn' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpSS61Z7/R.INSTALL8e430d52897/vsn/man/meanSdPlot.Rd:43: file link 'stat_binhex' in package 'ggplot2' does not exist and so has been treated as a topic
  Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpSS61Z7/R.INSTALL8e430d52897/vsn/man/meanSdPlot.Rd:44: file link 'stat_binhex' in package 'ggplot2' does not exist and so has been treated as a topic
See 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/vsn.Rcheck/00install.out' for details.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/vsn/libs/i386/vsn.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/vsn.Rcheck/00check.log'
for details.

Installation output

vsn.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/vsn_3.55.0.tar.gz && rm -rf vsn.buildbin-libdir && mkdir vsn.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vsn.buildbin-libdir vsn_3.55.0.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL vsn_3.55.0.zip && rm vsn_3.55.0.tar.gz vsn_3.55.0.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  436k  100  436k    0     0  1202k      0 --:--:-- --:--:-- --:--:-- 1225k

install for i386

* installing *source* package 'vsn' ...
** using staged installation
** libs
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vsn.c -o vsn.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vsn2.c -o vsn2.o
/mingw32/bin/gcc -shared -s -static-libgcc -o vsn.dll tmp.def init.o vsn.o vsn2.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/vsn.buildbin-libdir/00LOCK-vsn/00new/vsn/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'vsn'
    finding HTML links ... done
    class.vsn                               html  
    class.vsnInput                          html  
    justvsn                                 html  
    kidney                                  html  
    lymphoma                                html  
    meanSdPlot                              html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpSS61Z7/R.INSTALL8e430d52897/vsn/man/meanSdPlot.Rd:43: file link 'stat_binhex' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpSS61Z7/R.INSTALL8e430d52897/vsn/man/meanSdPlot.Rd:44: file link 'stat_binhex' in package 'ggplot2' does not exist and so has been treated as a topic
    normalize.AffyBatch.vsn                 html  
    sagmbSimulateData                       html  
    scalingFactorTransformation             html  
    vsn-package                             html  
    vsn2                                    html  
    vsn2trsf                                html  
    vsnLikelihood                           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 'vsn' ...
** libs
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vsn.c -o vsn.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vsn2.c -o vsn2.o
/mingw64/bin/gcc -shared -s -static-libgcc -o vsn.dll tmp.def init.o vsn.o vsn2.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/vsn.buildbin-libdir/vsn/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vsn' as vsn_3.55.0.zip
* DONE (vsn)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'vsn' successfully unpacked and MD5 sums checked

Tests output

vsn.Rcheck/tests_i386/testthat.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 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("vsn")
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> test_check("vsn")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   2.93    0.20    3.12

vsn.Rcheck/tests_x64/testthat.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 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("vsn")
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> test_check("vsn")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   2.89    0.12    3.00

Example timings

vsn.Rcheck/examples_i386/vsn-Ex.timings

nameusersystemelapsed
class.vsn0.230.020.25
justvsn0.950.091.05
kidney0.050.000.05
lymphoma0.030.000.03
meanSdPlot1.000.003.56
normalize.AffyBatch.vsn000
sagmbSimulateData1.460.001.45
scalingFactorTransformation000
vsn20.280.040.31
vsn2trsf0.060.000.07
vsnLikelihood2.50.02.5

vsn.Rcheck/examples_x64/vsn-Ex.timings

nameusersystemelapsed
class.vsn0.250.000.25
justvsn1.210.011.24
kidney0.030.000.03
lymphoma0.030.000.03
meanSdPlot0.650.000.66
normalize.AffyBatch.vsn000
sagmbSimulateData1.190.001.18
scalingFactorTransformation000
vsn20.30.00.3
vsn2trsf0.050.000.05
vsnLikelihood2.480.002.48