BioC 3.2: CHECK report for annaffy on linux1.bioconductor.org

Package: annaffy

Version: 1.42.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings annaffy_1.42.0.tar.gz

StartedAt: 2015-10-27 00:59:20 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:00:34 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 73.8 seconds

RetCode: 0

Status:  OK

CheckDir: annaffy.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings annaffy_1.42.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/annaffy.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.42.0’
* 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 ... [7s/7s] 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 ‘dbGetQuery’
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 global function definition for ‘userQuery’
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’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/annaffy.Rcheck/00check.log’
for details.

* installing *source* package ‘annaffy’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annaffy)

name	user	system	elapsed
aafChromLoc	0.375	0.019	0.400
aafChromosome	0.042	0.000	0.043
aafCytoband	0.036	0.004	0.039
aafDescription	0.033	0.000	0.033
aafGO	0.629	0.024	0.661
aafGenBank	0.056	0.004	0.062
aafLocusLink	0.066	0.000	0.067
aafPathway	0.588	0.000	0.588
aafProbe	0.039	0.004	0.043
aafPubMed	0.229	0.008	0.293
aafSearchText	0.966	0.020	0.990
aafSymbol	0.176	0.000	0.177
aafUniGene	0.041	0.000	0.042
is.annpkg	0.749	0.068	0.826