Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for AnnotationHubData on tokay2

This page was generated on 2017-10-18 14:25:09 -0400 (Wed, 18 Oct 2017).

Package 53/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.6.2
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/AnnotationHubData
Branch: RELEASE_3_5
Last Commit: 9e461b5
Last Changed Date: 2017-10-11 08:20:34 -0400 (Wed, 11 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationHubData
Version: 1.6.2
Command: rm -rf AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && mkdir AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationHubData.buildbin-libdir AnnotationHubData_1.6.2.tar.gz >AnnotationHubData.Rcheck\00install.out 2>&1 && cp AnnotationHubData.Rcheck\00install.out AnnotationHubData-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AnnotationHubData.buildbin-libdir --install="check:AnnotationHubData-install.out" --force-multiarch --no-vignettes --timings AnnotationHubData_1.6.2.tar.gz
StartedAt: 2017-10-17 22:01:56 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:10:23 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 506.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AnnotationHubData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && mkdir AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationHubData.buildbin-libdir AnnotationHubData_1.6.2.tar.gz >AnnotationHubData.Rcheck\00install.out 2>&1 && cp AnnotationHubData.Rcheck\00install.out AnnotationHubData-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AnnotationHubData.buildbin-libdir --install="check:AnnotationHubData-install.out" --force-multiarch --no-vignettes --timings AnnotationHubData_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationHubData.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationHubData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHubData' version '1.6.2'
* package encoding: UTF-8
* 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 'AnnotationHubData' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocInstaller'
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
'library' or 'require' call to 'BiocInstaller' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: 'AnnotationHub:::.db_connection'
Unexported object imported by a ':::' call: 'OrganismDbi:::.packageTaxIds'
  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 ... NOTE
.NCBIMetadataFromUrl: no visible binding for global variable 'results'
.NCBIMetadataFromUrl: no visible binding for global variable 'specData'
.makeComplexGR: no visible binding for global variable 'seqname'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Title'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Description'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'BiocVersion'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Genome'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'SourceType'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'SourceUrl'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'SourceVersion'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Species'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'TaxonomyId'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Coordinate_1_based'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'DataProvider'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Maintainer'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'RDataClass'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'RDataDateAdded'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'RDataPath'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'DispatchClass'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Location_Prefix'
test_BioPaxImportPreparer_recipe: no visible binding for global
  variable 'ahroot'
test_BioPaxImportPreparer_recipe: no visible binding for global
  variable 'BiocVersion'
test_BioPaxImportPreparer_recipe: no visible global function definition
  for 'checkTrue'
test_Inparanoid8ImportPreparer_recipe: no visible global function
  definition for 'suppresWarnings'
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
  variable 'ahroot'
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
  variable 'BiocVersion'
test_Inparanoid8ImportPreparer_recipe: no visible global function
  definition for 'checkTrue'
trackWithAuxiliaryTablesToGRanges: no visible binding for global
  variable 'seqname'
Undefined global functions or variables:
  BiocVersion Coordinate_1_based DataProvider Description DispatchClass
  Genome Location_Prefix Maintainer RDataClass RDataDateAdded RDataPath
  SourceType SourceUrl SourceVersion Species TaxonomyId Title ahroot
  checkTrue results seqname specData suppresWarnings
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'AnnotationHubMetadata-class' but not in code:
  jsonPath constructAnnotationHubMetadataFromSourceFilePath
  constructMetadataFromJsonPath

* checking Rd \usage sections ... OK
* 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'AnnotationHubData_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'AnnotationHubData_unit_tests.R'
 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.


AnnotationHubData.Rcheck/00install.out:


install for i386

* installing *source* package 'AnnotationHubData' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'AnnotationHubData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationHubData' as AnnotationHubData_1.6.2.zip
* DONE (AnnotationHubData)

AnnotationHubData.Rcheck/examples_i386/AnnotationHubData-Ex.timings:

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class000
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
readMetadataFromCsv000
updateResources000
upload_to_S3000

AnnotationHubData.Rcheck/examples_x64/AnnotationHubData-Ex.timings:

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class000
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
readMetadataFromCsv000
updateResources000
upload_to_S3000