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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VegaMC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VegaMC_3.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VegaMC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VegaMC’ version ‘3.44.0’
* 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 ‘VegaMC’ can be installed ... WARNING
Found the following significant warnings:
  run_vegaMC.c:144:62: warning: data argument not used by format string [-Wformat-extra-args]
  run_vegaMC.c:150:13: warning: data argument not used by format string [-Wformat-extra-args]
  run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    example   4.9Mb
* 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 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGenes: no visible global function definition for ‘write.table’
qvalue: no visible global function definition for ‘smooth.spline’
qvalue: no visible global function definition for ‘predict’
vegaMC,character: no visible global function definition for
  ‘read.table’
vegaMC,character: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  predict read.table smooth.spline write.table
Consider adding
  importFrom("stats", "predict", "smooth.spline")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) vegaMC-methods.Rd:55: Lost braces
    55 |     \item{output_file_name}{(Default code{output}) File name used 
       |                                          ^
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/VegaMC/libs/VegaMC.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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 nor [v]sprintf. 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck/00check.log’
for details.