Package: ExperimentHubData

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ExperimentHubData_1.6.0.tar.gz

StartedAt: 2018-10-17 01:54:55 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:59:54 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 298.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ExperimentHubData.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ExperimentHubData_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ExperimentHubData.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ExperimentHubData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ExperimentHubData' version '1.6.0'
* 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 'ExperimentHubData' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpU7aJA3/R.INSTALL126062b363e5/ExperimentHubData/man/addResources.Rd:62: file link 'AnnotationHubMetadata' in package 'AnnotationHubData' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ExperimentHubData.Rcheck/00install.out' for details.
* 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
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'Title'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'Description'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'BiocVersion'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'Genome'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'SourceType'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'SourceUrl'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'SourceVersion'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'Species'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'TaxonomyId'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'Coordinate_1_based'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'DataProvider'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'Maintainer'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'RDataClass'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'RDataDateAdded'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'RDataPath'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'DispatchClass'
makeExperimentHubMetadata : <anonymous>: no visible binding for global
  variable 'PreparerClass'
Undefined global functions or variables:
  BiocVersion Coordinate_1_based DataProvider Description DispatchClass
  Genome Maintainer PreparerClass RDataClass RDataDateAdded RDataPath
  SourceType SourceUrl SourceVersion Species TaxonomyId Title
* 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 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ExperimentHubData.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ExperimentHubData_1.6.0.tar.gz && rm -rf ExperimentHubData.buildbin-libdir && mkdir ExperimentHubData.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ExperimentHubData.buildbin-libdir ExperimentHubData_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ExperimentHubData_1.6.0.zip && rm ExperimentHubData_1.6.0.tar.gz ExperimentHubData_1.6.0.zip
###
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install for i386

* installing *source* package 'ExperimentHubData' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ExperimentHubData'
    finding HTML links ... done
    ExperimentHubMetadata-class             html  
    addResources                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpU7aJA3/R.INSTALL126062b363e5/ExperimentHubData/man/addResources.Rd:62: file link 'AnnotationHubMetadata' in package 'AnnotationHubData' does not exist and so has been treated as a topic
    makeExperimentHubMetadata               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ExperimentHubData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ExperimentHubData' as ExperimentHubData_1.6.0.zip
* DONE (ExperimentHubData)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ExperimentHubData' successfully unpacked and MD5 sums checked
In R CMD INSTALL