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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ToPASeq.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ToPASeq_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ToPASeq.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ToPASeq/DESCRIPTION’ ... OK
* this is package ‘ToPASeq’ version ‘1.24.0’
* package encoding: UTF-8
* 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 ‘ToPASeq’ can be installed ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
drawGraph: no visible global function definition for ‘renderGraph’
estimateCF: no visible global function definition for ‘buildGraphNEL’
makeLegend: no visible global function definition for ‘image’
makeLegend: no visible global function definition for ‘axis’
makeLegend: no visible global function definition for ‘mtext’
makeNodeSizeLegend: no visible global function definition for
  ‘layoutGraph’
makeNodeSizeLegend: no visible global function definition for
  ‘renderGraph’
plot.topResult: no visible global function definition for ‘reduceGraph’
plotCliques: no visible global function definition for ‘layoutGraph’
plotRagraph : .local: no visible binding for global variable
  ‘drawAgNode’
plotRagraph : .local: no visible global function definition for
  ‘graphLayout’
plotRagraph : .local: no visible global function definition for
  ‘upRight’
plotRagraph : .local: no visible global function definition for
  ‘boundBox’
plotRagraph : .local: no visible global function definition for
  ‘botLeft’
plotRagraph : .local: no visible global function definition for ‘getX’
plotRagraph : .local: no visible global function definition for ‘getY’
plotRagraph : .local: no visible global function definition for
  ‘AgNode’
plotRagraph : .local: no visible global function definition for
  ‘getNodeRW’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘getNodeRW’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘getNodeLW’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘getNodeHeight’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘labelText’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘txtLabel’
plotRagraph : .local: no visible global function definition for
  ‘AgEdge’
renderOrig: no visible global function definition for ‘layoutGraph’
renderReduced: no visible global function definition for ‘reduceGraph’
renderReduced: no visible global function definition for ‘layoutGraph’
renderSpline: no visible global function definition for ‘bezierPoints’
shadowtext: no visible global function definition for ‘xy.coords’
shadowtext: no visible global function definition for ‘grconvertX’
shadowtext: no visible global function definition for ‘grconvertY’
Undefined global functions or variables:
  AgEdge AgNode axis bezierPoints botLeft boundBox buildGraphNEL
  drawAgNode getNodeHeight getNodeLW getNodeRW getX getY graphLayout
  grconvertX grconvertY image labelText layoutGraph mtext reduceGraph
  renderGraph txtLabel upRight xy.coords
Consider adding
  importFrom("grDevices", "xy.coords")
  importFrom("graphics", "axis", "grconvertX", "grconvertY", "image",
             "mtext")
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 ... WARNING
Documented arguments not in \usage in documentation object 'res':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
TAPPA       7.532  0.076   7.612
CePa        6.892  0.176   7.200
PRS         6.724  0.028   6.788
PRS_wrapper 5.140  0.068   5.217
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ToPASeq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ToPASeq
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ToPASeq’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c accCpp.cpp -o accCpp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c betweeness.cpp -o betweeness.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c colMinMax.cpp -o colMinMax.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c downstream.cpp -o downstream.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o ToPASeq.so RcppExports.o accCpp.o betweeness.o colMinMax.o downstream.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-ToPASeq/00new/ToPASeq/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ToPASeq)