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CHECK report for annaffy on tokay1

This page was generated on 2020-08-10 12:10:06 -0400 (Mon, 10 Aug 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 55/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annaffy 1.61.0
Colin A. Smith
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/annaffy
Branch: master
Last Commit: ff79835
Last Changed Date: 2020-04-27 14:08:37 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: annaffy
Version: 1.61.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annaffy_1.61.0.tar.gz
StartedAt: 2020-08-09 23:41:51 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 23:47:43 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 351.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: annaffy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annaffy_1.61.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/annaffy.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annaffy/DESCRIPTION' ... OK
* this is package 'annaffy' version '1.61.0'
* 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 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 'C:/Users/biocbuild/bbs-3.12-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
is.annpkg 5.61    1.2   17.58
aafPubMed 0.20    0.1   64.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
is.annpkg 7.98   0.82    9.65
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/annaffy.Rcheck/00check.log'
for details.



Installation output

annaffy.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/annaffy_1.61.0.tar.gz && rm -rf annaffy.buildbin-libdir && mkdir annaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annaffy.buildbin-libdir annaffy_1.61.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL annaffy_1.61.0.zip && rm annaffy_1.61.0.tar.gz annaffy_1.61.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 71187  100 71187    0     0   235k      0 --:--:-- --:--:-- --:--:--  238k

install for i386

* 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
  converting help for package 'annaffy'
    finding HTML links ... done
    aaf.character                           html  
    aaf.goterm                              html  
    aaf.handler                             html  
    aaf.integer                             html  
    aaf.raw                                 html  
    aafChromLoc-class                       html  
    aafChromLoc                             html  
    aafChromosome-class                     html  
    aafChromosome                           html  
    aafCytoband-class                       html  
    aafCytoband                             html  
    aafDescription-class                    html  
    aafDescription                          html  
    aafExpr                                 html  
    aafGO-class                             html  
    aafGO                                   html  
    aafGOItem-class                         html  
    aafGenBank-class                        html  
    aafGenBank                              html  
    aafIntensity-class                      html  
    aafList-class                           html  
    aafLocusLink-class                      html  
    aafLocusLink                            html  
    aafPathway-class                        html  
    aafPathway                              html  
    aafPathwayItem-class                    html  
    aafProbe-class                          html  
    aafProbe                                html  
    aafPubMed-class                         html  
    aafPubMed                               html  
    aafSearchGO                             html  
    aafSearchText                           html  
    aafSigned-class                         html  
    aafSymbol-class                         html  
    aafSymbol                               html  
    aafTable-class                          html  
    aafTable                                html  
    aafTableAnn                             html  
    aafTableFrame                           html  
    aafTableInt                             html  
    aafUniGene-class                        html  
    aafUniGene                              html  
    chkPkgs                                 html  
    getCSS-methods                          html  
    getHTML-methods                         html  
    getTD-methods                           html  
    getText-methods                         html  
    getURL-methods                          html  
    is.annpkg                               html  
    selectorWidget                          html  
** 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

install for x64

* installing *source* package 'annaffy' ...
** testing if installed package can be loaded
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
* MD5 sums
packaged installation of 'annaffy' as annaffy_1.61.0.zip
* DONE (annaffy)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'annaffy' successfully unpacked and MD5 sums checked

Tests output


Example timings

annaffy.Rcheck/examples_i386/annaffy-Ex.timings

nameusersystemelapsed
aafChromLoc0.290.020.41
aafChromosome0.200.020.22
aafCytoband0.050.004.86
aafDescription0.030.000.03
aafGO0.150.060.22
aafGenBank0.030.010.73
aafLocusLink0.050.000.05
aafPathway0.380.082.53
aafProbe0.030.000.03
aafPubMed 0.20 0.1064.42
aafSearchText0.360.000.36
aafSymbol0.030.000.04
aafUniGene0.050.004.18
is.annpkg 5.61 1.2017.58

annaffy.Rcheck/examples_x64/annaffy-Ex.timings

nameusersystemelapsed
aafChromLoc0.410.030.43
aafChromosome0.320.010.35
aafCytoband0.060.000.07
aafDescription0.050.020.06
aafGO0.230.090.33
aafGenBank0.050.000.04
aafLocusLink0.030.020.05
aafPathway0.720.030.75
aafProbe0.030.000.03
aafPubMed0.140.020.15
aafSearchText0.510.010.53
aafSymbol0.030.000.03
aafUniGene0.020.030.05
is.annpkg7.980.829.65