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CHECK report for ssviz on tokay1

This page was generated on 2020-04-15 12:23:10 -0400 (Wed, 15 Apr 2020).

Package 1667/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ssviz 1.20.0
Diana Low
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ssviz
Branch: RELEASE_3_10
Last Commit: 9f0b36b
Last Changed Date: 2019-10-29 13:09:00 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ssviz
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ssviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ssviz_1.20.0.tar.gz
StartedAt: 2020-04-15 06:54:21 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:57:28 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 186.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ssviz.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ssviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ssviz_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ssviz.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ssviz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ssviz' version '1.20.0'
* 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 'ssviz' 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
Examples with CPU or elapsed time > 5s
          user system elapsed
plotPP   10.59   0.00   10.61
pingpong  8.93   0.01    8.96
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
pingpong  8.3   0.02    8.55
plotPP    8.2   0.00    8.20
* 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-3.10-bioc/meat/ssviz.Rcheck/00check.log'
for details.



Installation output

ssviz.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ssviz_1.20.0.tar.gz && rm -rf ssviz.buildbin-libdir && mkdir ssviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ssviz.buildbin-libdir ssviz_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ssviz_1.20.0.zip && rm ssviz_1.20.0.tar.gz ssviz_1.20.0.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  823k  100  823k    0     0  15.6M      0 --:--:-- --:--:-- --:--:-- 16.7M

install for i386

* installing *source* package 'ssviz' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ssviz'
    finding HTML links ... done
    counts                                  html  
    ctrlbam                                 html  
    getCountMatrix-methods                  html  
    getCountMatrix                          html  
    logicalORmissing-class                  html  
    ntfreq-methods                          html  
    ntfreq                                  html  
    pctrlbam                                html  
    pingpong-methods                        html  
    pingpong                                html  
    plotDistro-methods                      html  
    plotDistro                              html  
    plotFreq-methods                        html  
    plotFreq                                html  
    plotPP-methods                          html  
    plotPP                                  html  
    plotRegion-methods                      html  
    plotRegion                              html  
    ptreatbam                               html  
    readBam-methods                         html  
    readBam                                 html  
    ssviz-package                           html  
    treatbam                                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 'ssviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ssviz' as ssviz_1.20.0.zip
* DONE (ssviz)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ssviz' successfully unpacked and MD5 sums checked

Tests output


Example timings

ssviz.Rcheck/examples_i386/ssviz-Ex.timings

nameusersystemelapsed
getCountMatrix0.210.020.22
logicalORmissing-class000
ntfreq0.520.030.54
pingpong8.930.018.96
plotDistro0.380.020.39
plotFreq0.690.000.68
plotPP10.59 0.0010.61
plotRegion1.170.031.21
readBam0.420.000.48

ssviz.Rcheck/examples_x64/ssviz-Ex.timings

nameusersystemelapsed
getCountMatrix0.220.000.22
logicalORmissing-class000
ntfreq0.580.010.59
pingpong8.300.028.55
plotDistro0.500.010.52
plotFreq1.190.001.19
plotPP8.20.08.2
plotRegion1.180.021.19
readBam0.400.010.42