##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SICtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SICtools_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SICtools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SICtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SICtools’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Depends: includes the non-default packages:
  'Rsamtools', 'doParallel', 'Biostrings', 'stringr', 'matrixStats',
  'plyr', 'GenomicRanges', 'IRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SICtools’ can be installed ... WARNING
Found the following significant warnings:
  vcf.c:243:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body]
  bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body]
  errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
  md5.c:51:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  md5.c:67:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  md5.c:116:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  md5.c:155:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess]
  md5.c:176:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SICtools.Rcheck/00install.out’ for details.
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    FEATURES
  Cannot process chunk/lines:
    This package is to find SNV/Indel differences between two bam files with near relationship
  Cannot process chunk/lines:
    in a way of pairwise comparison thourgh each base position across the genome region of interest. 
  Cannot process chunk/lines:
    The difference is inferred by fisher test and euclidean distance, the input of which is the base
  Cannot process chunk/lines:
    count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both 
  Cannot process chunk/lines:
    sides of indel region.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.indelDiffFunc: no visible global function definition for ‘fisher.test’
.indelDiffFunc: no visible global function definition for ‘dist’
indelDiff: no visible global function definition for ‘read.delim’
snpDiff : calcInfoRange : <anonymous>: no visible global function
  definition for ‘fisher.test’
snpDiff : calcInfoRange : <anonymous>: no visible global function
  definition for ‘dist’
Undefined global functions or variables:
  dist fisher.test read.delim
Consider adding
  importFrom("stats", "dist", "fisher.test")
  importFrom("utils", "read.delim")
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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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 include directives in Makefiles ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SICtools.Rcheck/00check.log’
for details.