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CHECK report for annaffy on malbec2

This page was generated on 2020-10-17 11:54:22 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE annaffy PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 58/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annaffy 1.60.0
Colin A. Smith
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/annaffy
Branch: RELEASE_3_11
Last Commit: ed7e8ee
Last Changed Date: 2020-04-27 14:08:37 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: annaffy
Version: 1.60.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:annaffy.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings annaffy_1.60.0.tar.gz
StartedAt: 2020-10-16 22:46:24 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:47:52 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 87.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: annaffy.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:annaffy.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings annaffy_1.60.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/annaffy.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.60.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/annaffy.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
* 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 : <anonymous>: no visible global function definition for
  ‘tkset’
selectorWidget: no visible global function definition for ‘tkscrollbar’
selectorWidget : <anonymous>: 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 : <anonymous>: 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 (user + system) or elapsed time > 5s
           user system elapsed
is.annpkg 5.979  0.401   6.335
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/annaffy.Rcheck/00check.log’
for details.



Installation output

annaffy.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL annaffy
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘annaffy’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (annaffy)

Tests output


Example timings

annaffy.Rcheck/annaffy-Ex.timings

nameusersystemelapsed
aafChromLoc0.2040.0310.341
aafChromosome0.0770.0010.139
aafCytoband0.0260.0120.087
aafDescription0.0210.0080.028
aafGO0.2680.0600.511
aafGenBank0.0390.0040.083
aafLocusLink0.0320.0000.032
aafPathway0.4490.0040.488
aafProbe0.0210.0000.021
aafPubMed0.2040.0231.531
aafSearchText0.3710.0040.375
aafSymbol0.0360.0000.037
aafUniGene0.0340.0000.078
is.annpkg5.9790.4016.335