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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:myvariant.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings myvariant_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/myvariant.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘myvariant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘myvariant’ version ‘1.34.0’
* checking package namespace information ... NOTE
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* 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 ‘myvariant’ 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 code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convertColumn4csv: no visible binding for global variable ‘is’
.df2DF: no visible binding for global variable ‘as’
.getIndels: no visible binding for global variable ‘REF’
.getIndels: no visible binding for global variable ‘ALT’
.unnest.df : <anonymous>: no visible global function definition for
  ‘is’
.unnest.df : <anonymous>: no visible global function definition for
  ‘setNames’
MyVariant: no visible global function definition for ‘new’
formatHgvs: no visible global function definition for
  ‘seqlevelsStyle<-’
validMyVariantObject: no visible global function definition for ‘slot’
.request.get,MyVariant: no visible global function definition for
  ‘capture.output’
.request.post,MyVariant: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  ALT REF as capture.output is new seqlevelsStyle<- setNames slot
Consider adding
  importFrom("methods", "as", "is", "new", "slot")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output")
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 ... NOTE
Argument items with no description in Rd file 'getVariant.Rd':
  ‘...’
Argument items with no description in Rd file 'getVariants.Rd':
  ‘...’
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/myvariant.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL myvariant
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘myvariant’ ...
** using staged installation
** R
** inst
** 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 (myvariant)