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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rGADEM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rGADEM_2.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rGADEM.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rGADEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rGADEM’ version ‘2.52.0’
* 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 ‘rGADEM’ can be installed ... WARNING
Found the following significant warnings:
  background.c:31:13: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  read_matrix.c:27:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  read_seq.c:30:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/rGADEM.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 ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’ ‘methods’ ‘seqLogo’
A package should be listed in only one of these fields.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘GenomicRanges’
  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
File ‘rGADEM/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

GADEM: no visible global function definition for ‘seqlevels’
readGademPWMFile: no visible global function definition for ‘read.csv’
readPWMfile: no visible global function definition for ‘read.table’
readTransfacFile: no visible global function definition for
  ‘read.table’
[,gadem-ANY-ANY-ANY: no visible binding for global variable ‘ANY’
[,gadem-ANY-ANY-ANY : <anonymous>: no visible binding for global
  variable ‘gadem’
plot,gadem-ANY : <anonymous>: no visible global function definition for
  ‘makePWM’
plot,motif-ANY: no visible global function definition for ‘makePWM’
Undefined global functions or variables:
  ANY gadem makePWM read.csv read.table seqlevels
Consider adding
  importFrom("utils", "read.csv", "read.table")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 75968 Segmentation fault: 11  LANGUAGE=en _R_CHECK_INTERNALS2_=1 R_LIBS=/tmp/RtmpGKXT1b/RLIBS_dbd942ccd04f R_ENVIRON_USER='' R_LIBS_USER='NULL' R_LIBS_SITE='NULL' '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'rGADEM-Ex.Rout' 2>&1 < 'rGADEM-Ex.R'
 ERROR
Running examples in ‘rGADEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GADEM
> ### Title: Motif Analysis with rGADEM
> ### Aliases: GADEM
> ### Keywords: GADEM MOTIFS
> 
> ### ** Examples
> 
> 
> 	library(BSgenome.Hsapiens.UCSC.hg19)
> 	library(rtracklayer)
> 	BedFile<- system.file("extdata","Test_100.bed",package="rGADEM")
> 	Sequences<-import(BedFile)
> 	gadem<-GADEM(Sequences,verbose=1,genome=Hsapiens)
Retrieving sequences... Done.
*** Start C Programm ***
==============================================================================================
input sequence file:  
number of sequences and average length:				50 201.0
Use pgf method to approximate llr null distribution
parameters estimated from sequences in:  

number of GA generations & population size:			5 100

PWM score p-value cutoff for binding site declaration:		2.000000e-04
ln(E-value) cutoff for motif declaration:			0.000000

number of EM steps:						40
minimal no. sites considered for a motif:			2

[a,c,g,t] frequencies in input data:				0.289980 0.210020 0.210020 0.289980
==============================================================================================
*** Running an unseeded analysis ***
GADEM cycle  1: enumerate and count k-mers... top 3  4, 5-mers: 14 22 30
Done.
Initializing GA... Done.

 *** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
 1: GADEM(Sequences, verbose = 1, genome = Hsapiens)
An irrecoverable exception occurred. R is aborting now ...
* 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: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/rGADEM.Rcheck/00check.log’
for details.