Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-10-15 15:06:20 -0400 (Fri, 15 Oct 2021).

CHECK results for RUVnormalize on tokay2

To the developers/maintainers of the RUVnormalize package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RUVnormalize.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1656/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVnormalize 1.26.0  (landing page)
Laurent Jacob
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/RUVnormalize
git_branch: RELEASE_3_13
git_last_commit: b11bbc7
git_last_commit_date: 2021-05-19 12:06:46 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RUVnormalize
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RUVnormalize.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RUVnormalize_1.26.0.tar.gz
StartedAt: 2021-10-15 04:59:23 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 05:00:29 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 66.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RUVnormalize.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RUVnormalize.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RUVnormalize_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RUVnormalize.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 'RUVnormalize/DESCRIPTION' ... OK
* this is package 'RUVnormalize' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'spams'
* 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 'RUVnormalize' 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 ... NOTE
'library' or 'require' call to 'spams' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterativeRUV: no visible global function definition for 'kmeans'
myPalette: no visible global function definition for 'col2rgb'
myPalette: no visible global function definition for 'rgb'
svdPlot: no visible global function definition for 'pdf'
svdPlot: no visible global function definition for 'par'
svdPlot: no visible global function definition for 'points'
svdPlot: no visible global function definition for 'text'
svdPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  col2rgb dev.off kmeans par pdf points rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb")
  importFrom("graphics", "par", "points", "text")
  importFrom("stats", "kmeans")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/RUVnormalize.Rcheck/00check.log'
for details.



Installation output

RUVnormalize.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/RUVnormalize_1.26.0.tar.gz && rm -rf RUVnormalize.buildbin-libdir && mkdir RUVnormalize.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RUVnormalize.buildbin-libdir RUVnormalize_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RUVnormalize_1.26.0.zip && rm RUVnormalize_1.26.0.tar.gz RUVnormalize_1.26.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 43548  100 43548    0     0   277k      0 --:--:-- --:--:-- --:--:--  277k

install for i386

* installing *source* package 'RUVnormalize' ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RUVnormalize'
    finding HTML links ... done
    clScore                                 html  
    iterativeRUV                            html  
    naiveRandRUV                            html  
    naiveReplicateRUV                       html  
    svdPlot                                 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 'RUVnormalize' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RUVnormalize' as RUVnormalize_1.26.0.zip
* DONE (RUVnormalize)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'RUVnormalize' successfully unpacked and MD5 sums checked

Tests output


Example timings

RUVnormalize.Rcheck/examples_i386/RUVnormalize-Ex.timings

nameusersystemelapsed
clScore2.720.223.84
iterativeRUV0.060.000.06
naiveRandRUV2.440.092.54
naiveReplicateRUV1.790.111.91
svdPlot2.360.062.42

RUVnormalize.Rcheck/examples_x64/RUVnormalize-Ex.timings

nameusersystemelapsed
clScore2.690.353.03
iterativeRUV0.080.000.08
naiveRandRUV2.410.292.70
naiveReplicateRUV1.870.132.00
svdPlot2.410.082.48