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CHECK report for nudge on tokay2

This page was generated on 2018-06-06 10:10:47 -0400 (Wed, 06 Jun 2018).

Package 1004/1559HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nudge 1.46.0
N. Dean
Snapshot Date: 2018-06-05 16:45:51 -0400 (Tue, 05 Jun 2018)
URL: https://git.bioconductor.org/packages/nudge
Branch: RELEASE_3_7
Last Commit: 8a66b3f
Last Changed Date: 2018-04-30 10:35:04 -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: nudge
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings nudge_1.46.0.tar.gz
StartedAt: 2018-06-06 04:52:59 -0400 (Wed, 06 Jun 2018)
EndedAt: 2018-06-06 04:54:08 -0400 (Wed, 06 Jun 2018)
EllapsedTime: 69.1 seconds
RetCode: 0
Status:  OK  
CheckDir: nudge.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:nudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings nudge_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/nudge.Rcheck'
* using R version 3.5.0 Patched (2018-05-03 r74699)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nudge/DESCRIPTION' ... OK
* this is package 'nudge' version '1.46.0'
* 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 'nudge' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
norm2d 5.67   0.02    5.92
nudge2 4.71   0.02    5.01
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/nudge.Rcheck/00check.log'
for details.



Installation output

nudge.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/nudge_1.46.0.tar.gz && rm -rf nudge.buildbin-libdir && mkdir nudge.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nudge.buildbin-libdir nudge_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL nudge_1.46.0.zip && rm nudge_1.46.0.tar.gz nudge_1.46.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  774k  100  774k    0     0  13.8M      0 --:--:-- --:--:-- --:--:-- 15.4M

install for i386

* installing *source* package 'nudge' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nudge'
    finding HTML links ... done
    hiv                                     html  
    like                                    html  
    neg.contr                               html  
    norm1a                                  html  
    norm1b                                  html  
    norm1c                                  html  
    norm1d                                  html  
    norm2c                                  html  
    norm2d                                  html  
    nudge1                                  html  
    nudge2                                  html  
    pos.contr                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'nudge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nudge' as nudge_1.46.0.zip
* DONE (nudge)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'nudge' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

nudge.Rcheck/examples_i386/nudge-Ex.timings

nameusersystemelapsed
norm1a0.630.000.62
norm1b0.710.000.72
norm1c0.230.000.23
norm1d0.290.000.28
norm2c3.850.054.92
norm2d4.080.024.33
nudge11.350.011.36
nudge23.820.024.10

nudge.Rcheck/examples_x64/nudge-Ex.timings

nameusersystemelapsed
norm1a0.50.00.5
norm1b0.540.020.56
norm1c0.220.000.22
norm1d0.330.000.33
norm2c3.280.074.17
norm2d5.670.025.92
nudge11.370.001.38
nudge24.710.025.01