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CHECK report for geneplast on tokay1

This page was generated on 2019-04-13 11:26:48 -0400 (Sat, 13 Apr 2019).

Package 602/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneplast 1.8.0
Mauro Castro
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/geneplast
Branch: RELEASE_3_8
Last Commit: 4fde86d
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 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: geneplast
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplast.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings geneplast_1.8.0.tar.gz
StartedAt: 2019-04-13 02:29:01 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:31:02 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 120.1 seconds
RetCode: 0
Status:  OK  
CheckDir: geneplast.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplast.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings geneplast_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/geneplast.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 'geneplast/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geneplast' version '1.8.0'
* 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 '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-3.8-bioc/meat/geneplast.Rcheck/00check.log'
for details.



Installation output

geneplast.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/geneplast_1.8.0.tar.gz && rm -rf geneplast.buildbin-libdir && mkdir geneplast.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneplast.buildbin-libdir geneplast_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL geneplast_1.8.0.zip && rm geneplast_1.8.0.tar.gz geneplast_1.8.0.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
 28 2651k   28  768k    0     0  5532k      0 --:--:-- --:--:-- --:--:-- 5647k
100 2651k  100 2651k    0     0  14.2M      0 --:--:-- --:--:-- --:--:-- 14.4M

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_1.8.0.zip
* DONE (geneplast)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 -- Sat Apr 13 02:30:55 2019 
*********************************************** 
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 
   3.46    0.15    3.62 

geneplast.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 -- Sat Apr 13 02:30:57 2019 
*********************************************** 
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 
   2.10    0.09    2.20 

Example timings

geneplast.Rcheck/examples_i386/geneplast-Ex.timings

nameusersystemelapsed
gpdata0.200.040.27
gplast0.490.010.50
gplast.get0.470.000.47
gplast.preprocess0.540.020.56
groot1.470.001.47
groot.get1.490.001.48
groot.plot1.710.011.74
groot.preprocess0.720.020.73
ogr2igraph000
ogr2tni000
ppidata0.000.000.05

geneplast.Rcheck/examples_x64/geneplast-Ex.timings

nameusersystemelapsed
gpdata0.170.010.19
gplast0.440.000.44
gplast.get0.450.000.45
gplast.preprocess0.450.000.46
groot2.320.022.34
groot.get1.790.001.80
groot.plot1.880.021.89
groot.preprocess0.780.000.78
ogr2igraph000
ogr2tni000
ppidata000