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CHECK report for sscu on tokay1

This page was generated on 2019-04-13 11:26:32 -0400 (Sat, 13 Apr 2019).

Package 1506/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sscu 2.12.0
Yu Sun
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/sscu
Branch: RELEASE_3_8
Last Commit: 50b310f
Last Changed Date: 2018-10-30 11:42:00 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: sscu
Version: 2.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sscu.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sscu_2.12.0.tar.gz
StartedAt: 2019-04-13 05:44:13 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:47:24 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 191.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: sscu.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sscu.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sscu_2.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sscu.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sscu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sscu' version '2.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'sscu' can be installed ... OK
* checking installed package size ... OK
* checking package 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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'sscu.Rmd'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/sscu.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
op_corre_NCprime 9.04   0.04    9.34
op_corre_CodonW  8.13   0.13    8.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
op_corre_CodonW  16.05   0.03   16.08
op_corre_NCprime 15.69   0.01   15.70
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/sscu.Rcheck/00check.log'
for details.



Installation output

sscu.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/sscu_2.12.0.tar.gz && rm -rf sscu.buildbin-libdir && mkdir sscu.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sscu.buildbin-libdir sscu_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sscu_2.12.0.zip && rm sscu_2.12.0.tar.gz sscu_2.12.0.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 1367k  100 1367k    0     0  17.2M      0 --:--:-- --:--:-- --:--:-- 18.0M

install for i386

* installing *source* package 'sscu' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sscu'
    finding HTML links ... done
    akashi_test                             html  
    genomic_gc3                             html  
    finding level-2 HTML links ... done

    low_frequency_op                        html  
    op_corre_CodonW                         html  
    op_corre_NCprime                        html  
    op_highly                               html  
    op_highly_stats                         html  
    s_index                                 html  
    sscu-package                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sscu' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sscu' as sscu_2.12.0.zip
* DONE (sscu)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'sscu' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

sscu.Rcheck/examples_i386/sscu-Ex.timings

nameusersystemelapsed
akashi_test0.000.000.03
genomic_gc30.160.010.40
low_frequency_op0.730.001.11
op_corre_CodonW8.130.138.34
op_corre_NCprime9.040.049.34
op_highly0.810.020.85
op_highly_stats0.830.000.83
s_index0.160.000.15

sscu.Rcheck/examples_x64/sscu-Ex.timings

nameusersystemelapsed
akashi_test0.020.000.02
genomic_gc30.220.000.22
low_frequency_op0.970.000.97
op_corre_CodonW16.05 0.0316.08
op_corre_NCprime15.69 0.0115.70
op_highly1.310.001.31
op_highly_stats1.260.001.27
s_index0.250.020.26