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CHECK report for annaffy on malbec2

This page was generated on 2019-10-16 11:55:10 -0400 (Wed, 16 Oct 2019).

Package 56/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annaffy 1.56.0
Colin A. Smith
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/annaffy
Branch: RELEASE_3_9
Last Commit: 8c8e16a
Last Changed Date: 2019-05-02 11:53:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annaffy
Version: 1.56.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:annaffy.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings annaffy_1.56.0.tar.gz
StartedAt: 2019-10-15 23:44:12 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 23:45:48 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 96.6 seconds
RetCode: 0
Status:  OK 
CheckDir: annaffy.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:annaffy.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings annaffy_1.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/annaffy.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annaffy/DESCRIPTION’ ... OK
* this is package ‘annaffy’ version ‘1.56.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘annaffy’ 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
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GO.db’ ‘KEGG.db’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: ‘Biobase:::biocReposList’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘annaffy/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.aaf.goterm: no visible binding for global variable ‘GOTERM’
aafGO: no visible global function definition for ‘GO_dbfile’
aafPathway: no visible binding for global variable ‘KEGGPATHID2NAME’
aafTableInt: no visible global function definition for ‘sampleNames’
aafTableInt: no visible global function definition for ‘featureNames’
aafTableInt: no visible global function definition for ‘exprs’
chkPkgs: no visible binding for global variable ‘contrib.url’
chkPkgs: no visible global function definition for ‘available.packages’
chkPkgs: no visible global function definition for ‘userQuery’
chkPkgs: no visible global function definition for ‘install.packages’
selectorWidget : move: no visible global function definition for
  ‘tkcurselection’
selectorWidget : move: no visible global function definition for
  ‘tclvalue’
selectorWidget : move: no visible global function definition for
  ‘tkget’
selectorWidget : move: no visible global function definition for
  ‘tkinsert’
selectorWidget : move: no visible global function definition for
  ‘tkdelete’
selectorWidget : move: no visible global function definition for
  ‘tkselection.clear’
selectorWidget : ok: no visible global function definition for ‘tkget’
selectorWidget : ok: no visible global function definition for
  ‘tkdestroy’
selectorWidget: no visible global function definition for ‘tktoplevel’
selectorWidget: no visible global function definition for ‘tkwm.title’
selectorWidget: no visible global function definition for
  ‘tkwm.resizable’
selectorWidget: no visible global function definition for ‘tkframe’
selectorWidget: no visible global function definition for ‘tklistbox’
selectorWidget : : no visible global function definition for
  ‘tkset’
selectorWidget: no visible global function definition for ‘tkscrollbar’
selectorWidget : : no visible global function definition for
  ‘tkyview’
selectorWidget: no visible global function definition for ‘tkgrid’
selectorWidget: no visible global function definition for ‘tklabel’
selectorWidget: no visible global function definition for ‘tkbutton’
selectorWidget: no visible global function definition for ‘tkinsert’
selectorWidget : : no visible global function definition for
  ‘tkdestroy’
selectorWidget: no visible global function definition for ‘tkbind’
selectorWidget: no visible global function definition for
  ‘tkwait.window’
getHTML,aafUniGene: no visible binding for global variable ‘text’
saveHTML,aafTable: no visible global function definition for
  ‘browseURL’
Undefined global functions or variables:
  GOTERM GO_dbfile KEGGPATHID2NAME available.packages browseURL
  contrib.url exprs featureNames install.packages sampleNames tclvalue
  text tkbind tkbutton tkcurselection tkdelete tkdestroy tkframe tkget
  tkgrid tkinsert tklabel tklistbox tkscrollbar tkselection.clear tkset
  tktoplevel tkwait.window tkwm.resizable tkwm.title tkyview userQuery
Consider adding
  importFrom("graphics", "text")
  importFrom("utils", "available.packages", "browseURL", "contrib.url",
             "install.packages")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
is.annpkg 6.68  0.356    7.13
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/annaffy.Rcheck/00check.log’
for details.



Installation output

annaffy.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL annaffy
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘annaffy’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (annaffy)

Tests output


Example timings

annaffy.Rcheck/annaffy-Ex.timings

nameusersystemelapsed
aafChromLoc0.3380.0000.346
aafChromosome0.1610.0040.169
aafCytoband0.0510.0040.139
aafDescription0.050.000.05
aafGO0.2850.0360.484
aafGenBank0.0620.0050.087
aafLocusLink0.0530.0040.057
aafPathway0.6670.0040.676
aafProbe0.0350.0040.039
aafPubMed0.2250.0281.211
aafSearchText0.8200.0080.830
aafSymbol0.0530.0000.052
aafUniGene0.0580.0000.139
is.annpkg6.6800.3567.130