Package: TSRchitect

Version: 1.12.4

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSRchitect.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TSRchitect_1.12.4.tar.gz

StartedAt: 2020-04-15 07:17:17 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:22:25 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 308.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TSRchitect.Rcheck

Warnings: 3

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSRchitect.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TSRchitect_1.12.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TSRchitect.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TSRchitect/DESCRIPTION' ... OK
* this is package 'TSRchitect' version '1.12.4'
* 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 'TSRchitect' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... WARNING
Empty or missing file 'demo/00Index'.
See sections 'The INDEX file' and 'Package subdirectories' in the
'Writing R Extensions' manual.
* checking package subdirectories ... WARNING
Subdirectory 'demo' contains no demos.
* 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
mergeSampleData,tssObject-numeric-numeric : mergeTSSdf: no visible
  binding for global variable 'TSS'
mergeSampleData,tssObject-numeric-numeric : mergeTSSdf: no visible
  binding for global variable 'nTAGs'
Undefined global functions or variables:
  TSS nTAGs
* 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 ... WARNING
Undocumented arguments in documentation object 'determineTSR'
  '...'

Undocumented arguments in documentation object 'loadTSSobj'
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/TSRchitect.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TSRchitect_1.12.4.tar.gz && rm -rf TSRchitect.buildbin-libdir && mkdir TSRchitect.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TSRchitect.buildbin-libdir TSRchitect_1.12.4.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TSRchitect_1.12.4.zip && rm TSRchitect_1.12.4.tar.gz TSRchitect_1.12.4.zip
###
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install for i386

* installing *source* package 'TSRchitect' ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TSRchitect'
    finding HTML links ... done
    TSRchitectUsersGuide                    html  
    TSRmshapeIndex                          html  
    TSRshapeIndex                           html  
    addAnnotationToTSR-methods              html  
    finding level-2 HTML links ... done

    addTagCountsToTSR-methods               html  
    bedToTSS-methods                        html  
    createSummarizedExperiment-methods      html  
    detTSR-methods                          html  
    determineTSR-methods                    html  
    getBamDataFirstRead-methods             html  
    getBamDataLastRead-methods              html  
    getFileNames-methods                    html  
    getTSRdata-methods                      html  
    getTSScountData-methods                 html  
    getTSStagData-methods                   html  
    getTitle-methods                        html  
    gsq2bed-methods                         html  
    importAnnotationExternal-methods        html  
    importAnnotationHub-methods             html  
    inputToTSS-methods                      html  
    loadTSSobj-methods                      html  
    makeGRangesFromTSR-methods              html  
    mergeSampleData-methods                 html  
    prcTSS                                  html  
    processTSS-methods                      html  
    tagCountTSS                             html  
    tsrCluster                              html  
    tssArrayProperties                      html  
    tssObject                               html  
    writeTSR-methods                        html  
    writeTSS-methods                        html  
** building package indices
** installing vignettes
   'TSRchitect.Rmd' using 'UTF-8' 
   'TSRchitectUsersGuide.Rmd' using 'UTF-8' 
** 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 'TSRchitect' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSRchitect' as TSRchitect_1.12.4.zip
* DONE (TSRchitect)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TSRchitect' successfully unpacked and MD5 sums checked