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CHECK report for RDRToolbox on tokay2

This page was generated on 2019-04-09 11:58:26 -0400 (Tue, 09 Apr 2019).

Package 1313/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RDRToolbox 1.33.1
Christoph Bartenhagen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/RDRToolbox
Branch: master
Last Commit: 9601c87
Last Changed Date: 2019-01-22 10:50:04 -0400 (Tue, 22 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: RDRToolbox
Version: 1.33.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RDRToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RDRToolbox_1.33.1.tar.gz
StartedAt: 2019-04-09 05:18:23 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:19:31 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 68.2 seconds
RetCode: 0
Status:  OK  
CheckDir: RDRToolbox.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RDRToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RDRToolbox_1.33.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RDRToolbox.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RDRToolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RDRToolbox' version '1.33.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'RDRToolbox' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
plotDR 5.42   0.03    5.46
Isomap 5.03   0.03    5.06
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/RDRToolbox.Rcheck/00check.log'
for details.



Installation output

RDRToolbox.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RDRToolbox_1.33.1.tar.gz && rm -rf RDRToolbox.buildbin-libdir && mkdir RDRToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RDRToolbox.buildbin-libdir RDRToolbox_1.33.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RDRToolbox_1.33.1.zip && rm RDRToolbox_1.33.1.tar.gz RDRToolbox_1.33.1.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 44452  100 44452    0     0   612k      0 --:--:-- --:--:-- --:--:--  678k

install for i386

* installing *source* package 'RDRToolbox' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RDRToolbox'
    finding HTML links ... done
    DBIndex                                 html  
    Isomap                                  html  
    LLE                                     html  
    SwissRoll                               html  
    generateData                            html  
    plotDR                                  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 'RDRToolbox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RDRToolbox' as RDRToolbox_1.33.1.zip
* DONE (RDRToolbox)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RDRToolbox' successfully unpacked and MD5 sums checked

Tests output


Example timings

RDRToolbox.Rcheck/examples_i386/RDRToolbox-Ex.timings

nameusersystemelapsed
DBIndex000
Isomap5.030.035.06
LLE3.650.053.71
SwissRoll000
generateData2.990.033.01
plotDR5.420.035.46

RDRToolbox.Rcheck/examples_x64/RDRToolbox-Ex.timings

nameusersystemelapsed
DBIndex000
Isomap3.190.083.26
LLE1.780.011.80
SwissRoll000
generateData1.600.021.61
plotDR3.780.043.83