Package: omicade4

Version: 1.22.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:omicade4.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings omicade4_1.22.0.tar.gz

StartedAt: 2019-04-13 04:15:06 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:16:57 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 111.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: omicade4.Rcheck

Warnings: 1

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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:omicade4.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings omicade4_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/omicade4.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 'omicade4/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'omicade4' version '1.22.0'
* 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 'omicade4' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4m48iP/R.INSTALL130022ed5fa3/omicade4/man/omicade4-package.Rd:48: file link 'ade4' in package 'ade4' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/omicade4.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  'ade4:::t.dudi' 'made4:::dudi.rwcoa' 'made4:::getdata'
  See the note in ?`:::` about the use of this operator.
* 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 installed files from 'inst/doc' ... 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/omicade4.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/omicade4_1.22.0.tar.gz && rm -rf omicade4.buildbin-libdir && mkdir omicade4.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=omicade4.buildbin-libdir omicade4_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL omicade4_1.22.0.zip && rm omicade4_1.22.0.tar.gz omicade4_1.22.0.zip
###
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install for i386

* installing *source* package 'omicade4' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'omicade4'
    finding HTML links ... done
    NCI60_4arrays                           html  
    mcia                                    html  
    omicade4-package                        html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4m48iP/R.INSTALL130022ed5fa3/omicade4/man/omicade4-package.Rd:48: file link 'ade4' in package 'ade4' does not exist and so has been treated as a topic
    plotVar                                 html  
    plotVar.cia                             html  
    plotVar.mcia                            html  
    selectVar                               html  
    selectVar.cia                           html  
    selectVar.mcia                          html  
    topVar                                  html  
    topVar.cia                              html  
    topVar.mcia                             html  
** building package indices
** installing vignettes
   'omicade4.Rnw' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'omicade4' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'omicade4' as omicade4_1.22.0.zip
* DONE (omicade4)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'omicade4' successfully unpacked and MD5 sums checked
In R CMD INSTALL