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CHECK report for KinSwingR on tokay1

This page was generated on 2019-04-13 11:29:47 -0400 (Sat, 13 Apr 2019).

Package 822/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KinSwingR 1.0.3
Ashley J. Waardenberg
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/KinSwingR
Branch: RELEASE_3_8
Last Commit: d7df7ee
Last Changed Date: 2018-11-12 02:46:34 -0400 (Mon, 12 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 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: KinSwingR
Version: 1.0.3
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KinSwingR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings KinSwingR_1.0.3.tar.gz
StartedAt: 2019-04-13 03:20:44 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:23:21 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 156.3 seconds
RetCode: 0
Status:  OK  
CheckDir: KinSwingR.Rcheck
Warnings: 0

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:KinSwingR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings KinSwingR_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/KinSwingR.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 'KinSwingR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KinSwingR' version '1.0.3'
* package encoding: UTF-8
* 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 'KinSwingR' 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 ... 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
swing          0.75   0.08   19.64
scoreSequences 0.54   0.05    8.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
swing          0.59   0.18   19.36
scoreSequences 0.47   0.07    8.16
* 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: OK


Installation output

KinSwingR.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/KinSwingR_1.0.3.tar.gz && rm -rf KinSwingR.buildbin-libdir && mkdir KinSwingR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KinSwingR.buildbin-libdir KinSwingR_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL KinSwingR_1.0.3.zip && rm KinSwingR_1.0.3.tar.gz KinSwingR_1.0.3.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  284k  100  284k    0     0  7249k      0 --:--:-- --:--:-- --:--:-- 7910k

install for i386

* installing *source* package 'KinSwingR' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KinSwingR'
    finding HTML links ... done
    KinSwingR                               html  
    buildPWM                                html  
    cleanAnnotation                         html  
    example_phosphoproteome                 html  
    phosphositeplus_human                   html  
    scoreSequences                          html  
    swing                                   html  
    viewPWM                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'KinSwingR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KinSwingR' as KinSwingR_1.0.3.zip
* DONE (KinSwingR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'KinSwingR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

KinSwingR.Rcheck/examples_i386/KinSwingR-Ex.timings

nameusersystemelapsed
buildPWM0.330.030.36
cleanAnnotation0.170.030.21
scoreSequences0.540.058.47
swing 0.75 0.0819.64
viewPWM0.320.000.31

KinSwingR.Rcheck/examples_x64/KinSwingR-Ex.timings

nameusersystemelapsed
buildPWM0.370.000.38
cleanAnnotation0.140.040.17
scoreSequences0.470.078.16
swing 0.59 0.1819.36
viewPWM0.340.000.34