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### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings contiBAIT_1.31.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/contiBAIT.Rcheck’
* using R Under development (unstable) (2024-01-16 r85812)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘contiBAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘contiBAIT’ version ‘1.31.1’
* 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 ‘contiBAIT’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'contiBAIT' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.19-bioc/meat/contiBAIT.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      1.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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
ideogramPlot.func: no visible binding for global variable ‘w’
ideogramPlot.func: no visible binding for global variable ‘w2’
makeChrTable: no visible global function definition for ‘queryHits’
makeChrTable: no visible global function definition for ‘subjectHits’
orderContigsGreedy: no visible global function definition for
  ‘makeCluster’
orderContigsGreedy: no visible global function definition for
  ‘clusterCall’
orderContigsGreedy: no visible global function definition for
  ‘stopCluster’
strandSeqFreqTable: no visible global function definition for
  ‘queryHits’
strandSeqFreqTable: no visible global function definition for
  ‘subjectHits’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
  binding for global variable ‘w’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
  binding for global variable ‘w2’
Undefined global functions or variables:
  clusterCall makeCluster queryHits stopCluster subjectHits w w2
* 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 Rd file 'plotLGDistances-LinkageGroupList-StrandStateMatrix-method.Rd':
  ‘...’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
findSimilarLibraries 10.155  2.819  12.664
contiBAIT             7.903  0.973   8.643
* 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: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD INSTALL contiBAIT
###
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* installing to library ‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library’
* installing *source* package ‘contiBAIT’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c buildLinkageGroups.cpp -o buildLinkageGroups.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c computeSim.cpp -o computeSim.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-devel_2024-01-16_r85812/lib -L/usr/local/lib -o contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/R/R-devel_2024-01-16_r85812/lib -lR
installing to /home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/00LOCK-contiBAIT/00new/contiBAIT/libs
** R
** data
** 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
Warning: Package 'contiBAIT' is deprecated and will be removed from Bioconductor
  version 3.20
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'contiBAIT' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (contiBAIT)