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CHECK report for sscu on tokay2

This page was generated on 2020-10-17 11:57:52 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE sscu PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1732/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sscu 2.18.0
Yu Sun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sscu
Branch: RELEASE_3_11
Last Commit: 42a2ff2
Last Changed Date: 2020-04-27 14:56:07 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: sscu
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sscu.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sscu_2.18.0.tar.gz
StartedAt: 2020-10-17 08:36:07 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:38:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 161.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: sscu.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sscu.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sscu_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/sscu.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.18.0'
* 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 '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 (user + system) or elapsed time > 5s
                  user system elapsed
op_corre_CodonW  16.03   0.20   16.86
op_corre_NCprime 12.39   0.07   12.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
op_corre_NCprime 12.07   0.05   12.10
op_corre_CodonW   9.81   0.03    9.85
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.11-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://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/sscu_2.18.0.tar.gz && rm -rf sscu.buildbin-libdir && mkdir sscu.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sscu.buildbin-libdir sscu_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sscu_2.18.0.zip && rm sscu_2.18.0.tar.gz sscu_2.18.0.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 1368k  100 1368k    0     0  20.1M      0 --:--:-- --:--:-- --:--:-- 22.6M

install for i386

* installing *source* package 'sscu' ...
** using staged installation
** 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 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 'sscu' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sscu' as sscu_2.18.0.zip
* DONE (sscu)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'sscu' successfully unpacked and MD5 sums checked

Tests output


Example timings

sscu.Rcheck/examples_i386/sscu-Ex.timings

nameusersystemelapsed
akashi_test0.010.000.01
genomic_gc30.290.000.43
low_frequency_op0.890.121.14
op_corre_CodonW16.03 0.2016.86
op_corre_NCprime12.39 0.0712.72
op_highly0.940.000.94
op_highly_stats1.110.001.11
s_index0.300.000.29

sscu.Rcheck/examples_x64/sscu-Ex.timings

nameusersystemelapsed
akashi_test000
genomic_gc30.130.050.17
low_frequency_op0.580.000.58
op_corre_CodonW9.810.039.85
op_corre_NCprime12.07 0.0512.10
op_highly0.860.010.88
op_highly_stats1.120.021.14
s_index0.140.040.19