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 3.3: CHECK report for AnnotationHubData on oaxaca

This page was generated on 2016-10-13 13:02:05 -0700 (Thu, 13 Oct 2016).

Package 49/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.2.2
Bioconductor Package Maintainer
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AnnotationHubData
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationHubData
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationHubData_1.2.2.tar.gz
StartedAt: 2016-10-12 23:16:53 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:32:23 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 930.3 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationHubData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationHubData_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/AnnotationHubData.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.2.2’
* 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 for sufficient/correct file permissions ... 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 ... 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
* 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
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’
jsonPath: no visible binding for global variable ‘SourceFile’
jsonPath: no visible binding for global variable ‘HubRoot’
pointer: no visible global function definition for ‘tail’
print.pointer: no visible global function definition for
  ‘capture.output’
print.pointer: no visible global function definition for ‘str’
ptr: no visible global function definition for ‘tail’
trackWithAuxiliaryTablesToGRanges: no visible binding for global
  variable ‘seqname’
Undefined global functions or variables:
  HubRoot SourceFile capture.output results seqname specData str tail
Consider adding
  importFrom("utils", "capture.output", "str", "tail")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.


AnnotationHubData.Rcheck/00install.out:

* 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
* DONE (AnnotationHubData)

AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings:

nameusersystemelapsed
AnnotationHubMetadata-class0.0040.0000.004
ImportPreparer-class0.0020.0000.002
makeEnsemblFasta0.0010.0000.001
makeGencodeFasta0.0010.0010.001
updateResources0.0020.0000.003
upload_to_S30.0010.0000.000