Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).

CHECK results for annaffy on machv2

To the developers/maintainers of the annaffy package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annaffy.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 59/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annaffy 1.64.2  (landing page)
Colin A. Smith
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/annaffy
git_branch: RELEASE_3_13
git_last_commit: e4b2445
git_last_commit_date: 2021-06-19 21:06:30 -0400 (Sat, 19 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: annaffy
Version: 1.64.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annaffy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annaffy_1.64.2.tar.gz
StartedAt: 2021-10-14 16:13:23 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 16:15:51 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 148.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: annaffy.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annaffy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annaffy_1.64.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/annaffy.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annaffy/DESCRIPTION’ ... OK
* this is package ‘annaffy’ version ‘1.64.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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:
  ‘Biobase’ ‘BiocManager’ ‘GO.db’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘BiocManager:::available’
  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
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’
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’
saveHTML,aafTable: no visible global function definition for
  ‘browseURL’
Undefined global functions or variables:
  GOTERM GO_dbfile browseURL exprs featureNames sampleNames tclvalue
  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("utils", "browseURL")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getURL-methods.Rd':
  ‘aafUniGene-class’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
is.annpkg 7.337   0.93   8.256
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/annaffy.Rcheck/00check.log’
for details.



Installation output

annaffy.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annaffy
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
aafChromLoc0.3470.0330.381
aafChromosome0.0810.0040.086
aafCytoband0.0460.0050.051
aafDescription0.0440.0060.049
aafGO0.4070.0910.524
aafGenBank0.0510.0070.059
aafLocusLink0.0570.0050.062
aafPathway0.0550.0090.064
aafProbe0.0410.0050.046
aafPubMed0.2160.0410.287
aafSearchText0.5840.0150.600
aafSymbol0.0380.0040.042
is.annpkg7.3370.9308.256