Package: BaseSpaceR

Version: 1.22.0

Command: rm -rf BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && mkdir BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BaseSpaceR.buildbin-libdir BaseSpaceR_1.22.0.tar.gz >BaseSpaceR.Rcheck\00install.out 2>&1 && cp BaseSpaceR.Rcheck\00install.out BaseSpaceR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BaseSpaceR.buildbin-libdir --install="check:BaseSpaceR-install.out" --force-multiarch --no-vignettes --timings BaseSpaceR_1.22.0.tar.gz

StartedAt: 2018-04-11 22:21:41 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:22:36 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 55.0 seconds

RetCode: 0

Status:  OK

CheckDir: BaseSpaceR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && mkdir BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BaseSpaceR.buildbin-libdir BaseSpaceR_1.22.0.tar.gz >BaseSpaceR.Rcheck\00install.out 2>&1 && cp BaseSpaceR.Rcheck\00install.out BaseSpaceR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BaseSpaceR.buildbin-libdir --install="check:BaseSpaceR-install.out" --force-multiarch --no-vignettes --timings BaseSpaceR_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BaseSpaceR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BaseSpaceR/DESCRIPTION' ... OK
* this is package 'BaseSpaceR' version '1.22.0'
* 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 'BaseSpaceR' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'Rsamtools' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
asBamFile: no visible global function definition for 'BamFile'
GET,ServiceURI: no visible global function definition for
  'basicHeaderGatherer'
GET,ServiceURI: no visible global function definition for
  'basicTextGatherer'
GET,ServiceURI: no visible global function definition for 'getForm'
GET,ServiceURI: no visible global function definition for 'curlOptions'
POST,ServiceURI: no visible global function definition for
  'basicHeaderGatherer'
POST,ServiceURI: no visible global function definition for
  'basicTextGatherer'
POST,ServiceURI: no visible global function definition for
  'curlPerform'
POSTForm,ServiceURI: no visible global function definition for
  'basicHeaderGatherer'
POSTForm,ServiceURI: no visible global function definition for
  'basicTextGatherer'
POSTForm,ServiceURI: no visible global function definition for
  'postForm'
POSTForm,ServiceURI: no visible global function definition for
  'curlOptions'
getBAMs,AppResults: no visible binding for global variable
  'BamFileList'
getFiles,AppAuth : .toDisk: no visible global function definition for
  'CFILE'
getFiles,AppAuth : .toDisk: no visible global function definition for
  'curlPerform'
getFiles,AppAuth : .toMem: no visible global function definition for
  'getURLContent'
getFiles,AppAuth : .toMem: no visible binding for global variable
  'dsize'
Undefined global functions or variables:
  BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer
  curlOptions curlPerform dsize getForm getURLContent postForm
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BaseSpaceR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BaseSpaceR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BaseSpaceR'
    finding HTML links ... done
    AppAuth-class                           html  
    AppResults-class                        html  
    AppSessionAuth                          html  
    AppSessions-class                       html  
    BaseSpaceR-package                      html  
    Coverage                                html  
    Error                                   html  
    Files-class                             html  
    FilesExtra                              html  
    Genomes-class                           html  
    Projects-class                          html  
    Response-class                          html  
    Runs-class                              html  
    Samples-class                           html  
    ServiceURI-class                        html  
    Users-class                             html  
    Variants                                html  
    data-aAuth                              html  
    private_methods                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BaseSpaceR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BaseSpaceR' as BaseSpaceR_1.22.0.zip
* DONE (BaseSpaceR)
In R CMD INSTALL
In R CMD INSTALL