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BioC 3.5: CHECK report for AnnotationFuncs on tokay2

This page was generated on 2017-10-18 14:21:08 -0400 (Wed, 18 Oct 2017).

Package 51/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationFuncs 1.26.0
Stefan McKinnon Edwards
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/AnnotationFuncs
Branch: RELEASE_3_5
Last Commit: ceca015
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationFuncs
Version: 1.26.0
Command: rm -rf AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && mkdir AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationFuncs.buildbin-libdir AnnotationFuncs_1.26.0.tar.gz >AnnotationFuncs.Rcheck\00install.out 2>&1 && cp AnnotationFuncs.Rcheck\00install.out AnnotationFuncs-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AnnotationFuncs.buildbin-libdir --install="check:AnnotationFuncs-install.out" --force-multiarch --no-vignettes --timings AnnotationFuncs_1.26.0.tar.gz
StartedAt: 2017-10-17 22:01:19 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:03:04 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 105.3 seconds
RetCode: 0
Status:  OK  
CheckDir: AnnotationFuncs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && mkdir AnnotationFuncs.buildbin-libdir AnnotationFuncs.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationFuncs.buildbin-libdir AnnotationFuncs_1.26.0.tar.gz >AnnotationFuncs.Rcheck\00install.out 2>&1 && cp AnnotationFuncs.Rcheck\00install.out AnnotationFuncs-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AnnotationFuncs.buildbin-libdir --install="check:AnnotationFuncs-install.out" --force-multiarch --no-vignettes --timings AnnotationFuncs_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationFuncs.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 'AnnotationFuncs/DESCRIPTION' ... OK
* this is package 'AnnotationFuncs' version '1.26.0'
* 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 'AnnotationFuncs' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field should not be empty
* 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
Package in Depends field not imported from: 'AnnotationDbi'
  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
getOrthologs: no visible global function definition for 'dbmeta'
getOrthologs: no visible global function definition for 'dbconn'
getOrthologs: no visible global function definition for 'dbfile'
getOrthologs: no visible global function definition for 'direction'
translate: no visible global function definition for 'dbmeta'
translate: no visible global function definition for 'dbconn'
translate: no visible global function definition for 'stack'
Undefined global functions or variables:
  dbconn dbfile dbmeta direction stack
Consider adding
  importFrom("utils", "stack")
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
getOrthologs 0.86   0.07    6.12
** 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationFuncs.Rcheck/00check.log'
for details.


AnnotationFuncs.Rcheck/00install.out:


install for i386

* installing *source* package 'AnnotationFuncs' ...
** 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 'AnnotationFuncs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationFuncs' as AnnotationFuncs_1.26.0.zip
* DONE (AnnotationFuncs)

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

nameusersystemelapsed
AnnotationFuncs-package1.020.032.44
getEvidenceCodes000
getOrthologs0.860.076.12
mapLists000
pickGO0.130.000.69
pickRefSeq0.060.010.12
removeNAs000
translate0.250.000.50

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

nameusersystemelapsed
AnnotationFuncs-package0.700.030.73
getEvidenceCodes000
getOrthologs0.650.000.64
mapLists000
pickGO0.060.000.07
pickRefSeq0.040.000.04
removeNAs000
translate0.140.030.17