Package: BiocCaseStudies

Version: 1.44.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocCaseStudies.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocCaseStudies_1.44.0.tar.gz

StartedAt: 2019-04-13 00:45:11 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:46:44 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 92.4 seconds

RetCode: 0

Status:  OK

CheckDir: BiocCaseStudies.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:BiocCaseStudies.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocCaseStudies_1.44.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocCaseStudies.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 'BiocCaseStudies/DESCRIPTION' ... OK
* this is package 'BiocCaseStudies' version '1.44.0'
* 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 'BiocCaseStudies' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  'Biobase' 'methods' 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fixedWidthCat: no visible global function definition for
  'capture.output'
fixedWidthCat: no visible global function definition for 'strbreak'
mySessionInfo: no visible global function definition for 'sessionInfo'
packages2install : <anonymous>: no visible global function definition
  for 'packageDescription'
packages2install : <anonymous>: no visible global function definition
  for 'is'
parseLibVers: no visible global function definition for
  'packageDescription'
requiredPackages : <anonymous>: no visible global function definition
  for 'packageDescription'
requiredPackages : <anonymous>: no visible global function definition
  for 'is'
resample: no visible global function definition for 'pData'
resample: no visible binding for global variable 'sd'
resample: no visible global function definition for 'plot'
resample: no visible global function definition for 'segments'
Undefined global functions or variables:
  capture.output is pData packageDescription plot sd segments
  sessionInfo strbreak
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("methods", "is")
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "packageDescription",
             "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocCaseStudies.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/BiocCaseStudies_1.44.0.tar.gz && rm -rf BiocCaseStudies.buildbin-libdir && mkdir BiocCaseStudies.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocCaseStudies.buildbin-libdir BiocCaseStudies_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BiocCaseStudies_1.44.0.zip && rm BiocCaseStudies_1.44.0.tar.gz BiocCaseStudies_1.44.0.zip
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100  6971  100  6971    0     0   174k      0 --:--:-- --:--:-- --:--:--  194k

install for i386

* installing *source* package 'BiocCaseStudies' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocCaseStudies'
    finding HTML links ... done
    fixedWidthCat                           html  
    markup                                  html  
    mySessionInfo                           html  
    parseLibVers                            html  
    requiredPackages                        html  
    resample                                html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BiocCaseStudies' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocCaseStudies' as BiocCaseStudies_1.44.0.zip
* DONE (BiocCaseStudies)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BiocCaseStudies' successfully unpacked and MD5 sums checked
In R CMD INSTALL