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CHECK report for geneplast on tokay2

This page was generated on 2018-10-17 08:42:25 -0400 (Wed, 17 Oct 2018).

Package 571/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneplast 1.6.2
Mauro Castro
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/geneplast
Branch: RELEASE_3_7
Last Commit: 19ddf5b
Last Changed Date: 2018-08-18 18:01:30 -0400 (Sat, 18 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneplast
Version: 1.6.2
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplast.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings geneplast_1.6.2.tar.gz
StartedAt: 2018-10-17 02:11:39 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:12:47 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 68.6 seconds
RetCode: 0
Status:  OK  
CheckDir: geneplast.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplast.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings geneplast_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/geneplast.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneplast/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geneplast' version '1.6.2'
* 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 'geneplast' 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 ... NOTE
Foreign function call to a different package:
  .C(node_height_clado, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/geneplast.Rcheck/00check.log'
for details.

Installation output

geneplast.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/geneplast_1.6.2.tar.gz && rm -rf geneplast.buildbin-libdir && mkdir geneplast.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneplast.buildbin-libdir geneplast_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL geneplast_1.6.2.zip && rm geneplast_1.6.2.tar.gz geneplast_1.6.2.zip
###
##############################################################################
##############################################################################


  % 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 2651k  100 2651k    0     0  29.3M      0 --:--:-- --:--:-- --:--:-- 32.3M

install for i386

* installing *source* package 'geneplast' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneplast'
    finding HTML links ... done
    OGP-class                               html  
    OGR-class                               html  
    geneplast-package                       html  
    gpdata                                  html  
    gplast                                  html  
    gplast.get                              html  
    gplast.preprocess                       html  
    groot                                   html  
    groot.get                               html  
    groot.plot                              html  
    groot.preprocess                        html  
    ogr2igraph                              html  
    ogr2tni                                 html  
    ppidata                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'geneplast' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneplast' as geneplast_1.6.2.zip
* DONE (geneplast)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'geneplast' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

geneplast.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("geneplast")
-Preprocessing for input data...

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-Preprocessing for input data...

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RUNIT TEST PROTOCOL -- Wed Oct 17 02:12:39 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geneplast RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.71    0.15    2.87

geneplast.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("geneplast")
-Preprocessing for input data...

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RUNIT TEST PROTOCOL -- Wed Oct 17 02:12:42 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geneplast RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   3.04    0.14    3.17

Example timings

geneplast.Rcheck/examples_i386/geneplast-Ex.timings

nameusersystemelapsed
gpdata0.270.000.32
gplast0.590.020.61
gplast.get0.420.020.44
gplast.preprocess0.460.000.45
groot1.610.011.63
groot.get1.730.001.75
groot.plot2.590.002.60
groot.preprocess0.570.010.58
ogr2igraph000
ogr2tni000
ppidata0.030.000.07

geneplast.Rcheck/examples_x64/geneplast-Ex.timings

nameusersystemelapsed
gpdata0.190.000.19
gplast0.460.030.49
gplast.get0.550.010.56
gplast.preprocess0.520.000.52
groot1.670.001.67
groot.get1.580.001.58
groot.plot2.50.02.5
groot.preprocess0.590.040.62
ogr2igraph000
ogr2tni000
ppidata000