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This page was generated on 2023-01-28 11:08:13 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for annaffy on merida1


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? 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 52/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annaffy 1.71.0  (landing page)
Colin A. Smith
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/annaffy
git_branch: master
git_last_commit: 02defd3
git_last_commit_date: 2022-11-01 10:35:52 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: annaffy
Version: 1.71.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annaffy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annaffy_1.71.0.tar.gz
StartedAt: 2023-01-27 22:20:10 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 22:24:55 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 285.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: annaffy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annaffy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annaffy_1.71.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/annaffy.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annaffy/DESCRIPTION’ ... OK
* this is package ‘annaffy’ version ‘1.71.0’
* 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:
  ‘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 ... NOTE
checkRd: (-1) aafTable-class.Rd:89: Escaped LaTeX specials: \$
* 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 14.418  1.377  21.064
* 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-3.17-bioc/meat/annaffy.Rcheck/00check.log’
for details.



Installation output

annaffy.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL annaffy
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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
aafChromLoc0.4140.0370.606
aafChromosome0.0990.0160.156
aafCytoband0.0950.0150.157
aafDescription0.0520.0060.079
aafGO0.4090.0760.659
aafGenBank0.0680.0070.093
aafLocusLink0.0600.0060.086
aafPathway0.0740.0080.104
aafProbe0.0390.0040.053
aafPubMed0.2720.0600.475
aafSearchText0.7990.0161.099
aafSymbol0.0870.0050.121
is.annpkg14.418 1.37721.064