Package: eudysbiome

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eudysbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings eudysbiome_1.12.0.tar.gz

StartedAt: 2019-04-13 02:07:13 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:10:06 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 173.7 seconds

RetCode: 0

Status:  OK

CheckDir: eudysbiome.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eudysbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings eudysbiome_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/eudysbiome.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 'eudysbiome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eudysbiome' version '1.12.0'
* 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 'eudysbiome' 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 ... NOTE
Cartesian: no visible global function definition for 'adjustcolor'
Cartesian: no visible global function definition for 'colors'
Cartesian: no visible global function definition for 'dev.hold'
Cartesian: no visible global function definition for 'dev.flush'
Cartesian: no visible global function definition for 'plot'
Cartesian: no visible global function definition for 'points'
Cartesian: no visible global function definition for 'abline'
Cartesian: no visible global function definition for 'axis'
Cartesian: no visible global function definition for 'text'
Cartesian: no visible global function definition for 'par'
Cartesian: no visible global function definition for 'mtext'
Cartesian: no visible global function definition for 'title'
Cartesian: no visible global function definition for 'rect'
assignTax: no visible global function definition for 'download.file'
assignTax: no visible global function definition for 'unzip'
assignTax: no visible global function definition for 'bunzip2'
contingencyTest: no visible global function definition for 'combn'
contingencyTest : <anonymous>: no visible global function definition
  for 'chisq.test'
microAnnotate: no visible global function definition for 'data'
microAnnotate: no visible binding for global variable 'harmGenera'
tableSpecies: no visible global function definition for 'read.table'
Undefined global functions or variables:
  abline adjustcolor axis bunzip2 chisq.test colors combn data
  dev.flush dev.hold download.file harmGenera mtext par plot points
  read.table rect text title unzip
Consider adding
  importFrom("grDevices", "adjustcolor", "colors", "dev.flush",
             "dev.hold")
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "points", "rect", "text", "title")
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn", "data", "download.file", "read.table",
             "unzip")
to your NAMESPACE file.
* 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 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/eudysbiome.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/eudysbiome_1.12.0.tar.gz && rm -rf eudysbiome.buildbin-libdir && mkdir eudysbiome.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=eudysbiome.buildbin-libdir eudysbiome_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL eudysbiome_1.12.0.zip && rm eudysbiome_1.12.0.tar.gz eudysbiome_1.12.0.zip
###
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install for i386

* installing *source* package 'eudysbiome' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'eudysbiome'
    finding HTML links ... done
    Cartesian                               html  
    assignTax                               html  
    contingencyCount                        html  
    contingencyTest                         html  
    diffGenera                              html  
    eudysbiome                              html  
    harmGenera                              html  
    microAnnotate                           html  
    microCount                              html  
    microDiff                               html  
    tableSpecies                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'eudysbiome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eudysbiome' as eudysbiome_1.12.0.zip
* DONE (eudysbiome)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'eudysbiome' successfully unpacked and MD5 sums checked
In R CMD INSTALL