##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vtpnet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vtpnet_0.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/vtpnet.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vtpnet/DESCRIPTION’ ... OK
* this is package ‘vtpnet’ version ‘0.46.0’
* 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 ‘vtpnet’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.1Mb
  sub-directories of 1Mb or more:
    data  20.0Mb
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘doParallel’ ‘foreach’
  Please remove these calls from your code.
'library' or 'require' call to ‘MotifDb’ 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:
  ‘doParallel’ ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rng2facHits: warning in dir(patt = "rda$"): partial argument match of
  'patt' to 'pattern'
runfimo: warning in dir(patt = "_out"): partial argument match of
  'patt' to 'pattern'
filterGWASbyMap: no visible global function definition for ‘as’
getMtags: no visible global function definition for ‘is’
getOneHits: no visible global function definition for ‘queryHits’
getOneHits: no visible global function definition for ‘subjectHits’
getOneHits: no visible global function definition for ‘metadata’
getOneHits: no visible global function definition for ‘metadata<-’
gwMatchPWM: no visible binding for global variable ‘Hsapiens’
gwMatchPWM: no visible global function definition for ‘is’
gwMatchPWM: no visible global function definition for ‘%dopar%’
gwMatchPWM: no visible global function definition for ‘foreach’
gwMatchPWM: no visible binding for global variable ‘i’
gwMatchPWM: no visible global function definition for ‘matchPWM’
gwMatchPWM: no visible global function definition for
  ‘PWMscoreStartingAt’
gwMatchPWM: no visible global function definition for ‘subject’
gwMatchPWM: no visible global function definition for ‘as’
rng2facHits: no visible global function definition for ‘as’
rng2facHits: no visible global function definition for
  ‘registerDoParallel’
rng2facHits: no visible global function definition for ‘%dopar%’
rng2facHits: no visible global function definition for ‘foreach’
rng2facHits: no visible binding for global variable ‘i’
runfimo: no visible global function definition for ‘%dopar%’
runfimo: no visible global function definition for ‘foreach’
runfimo: no visible binding for global variable ‘i’
setupGWPM: no visible global function definition for
  ‘registerDoParallel’
Undefined global functions or variables:
  %dopar% Hsapiens PWMscoreStartingAt as foreach i is matchPWM metadata
  metadata<- queryHits registerDoParallel subject subjectHits
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: vtpnet-package.Rd:48-50: Dropping empty section \references
prepare_Rd: vtpnet-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: vtpnet-package.Rd:55-56: Dropping empty section \examples
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/vtpnet.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘vtpnet’ ...
** 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 (vtpnet)