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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:vtpnet.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings vtpnet_0.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/vtpnet.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘vtpnet/DESCRIPTION’ ... OK
* this is package ‘vtpnet’ version ‘0.39.0’
* 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 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
Killed
* 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 files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vtpnet.Rnw’... OK
 OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘vtpnet.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:Rgraphviz’:

    from, to

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: gwascat
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Killed

* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/vtpnet.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL vtpnet
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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)