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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:goseq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings goseq_1.47.0.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/goseq.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'goseq/DESCRIPTION' ... OK
* this is package 'goseq' version '1.47.0'
* 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 'goseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 'rtracklayer' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for 'winMenuAddItem'
getlength: no visible global function definition for
  'installed.packages'
getlength: no visible global function definition for 'tail'
getlength: no visible global function definition for
  'transcriptLengths'
getlength: no visible global function definition for 'browserSession'
getlength: no visible global function definition for 'genome<-'
getlength: no visible global function definition for 'ucscTableQuery'
getlength: no visible global function definition for 'getTable'
makespline: no visible global function definition for 'show'
supportedOrganisms: no visible global function definition for
  'ucscGenomes'
Undefined global functions or variables:
  browserSession genome<- getTable installed.packages show tail
  transcriptLengths ucscGenomes ucscTableQuery winMenuAddItem
Consider adding
  importFrom("methods", "show")
  importFrom("utils", "installed.packages", "tail", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
goseq     27.39   4.11   37.94
getgo     10.96   1.14   12.11
nullp      9.39   1.99   14.71
plotPWF    8.79   2.29   13.28
getlength  6.25   2.09    8.34
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/goseq.Rcheck/00check.log'
for details.

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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL goseq
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'goseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'goseq'
    finding HTML links ... done
    genes                                   html  
    getgo                                   html  
    finding level-2 HTML links ... done

    getlength                               html  
    goseq                                   html  
    makespline                              html  
    nullp                                   html  
    plotPWF                                 html  
    supportedOrganisms                      html  
** 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 (goseq)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'hiAnnotator' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'txcutr' is missing or broken
 done