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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNEr_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNEr.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.30.0’
* 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 ‘CNEr’ can be installed ... WARNING
Found the following significant warnings:
  ucsc/common.c:2842:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2843:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2844:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2845:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2846:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2847:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2848:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2849:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2976:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2977:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2978:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2979:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2980:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2981:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2982:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2983:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNEr.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 17.6Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... 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
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/CNEr/libs/CNEr.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
makeGRBs     447.58  3.862 451.970
plotCNEWidth  12.60  0.477  13.084
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNEr.Rcheck/00check.log’
for details.