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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings casper_2.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/casper.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.41.0’
* 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'
 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 ‘casper’ can be installed ... WARNING
Found the following significant warnings:
  cstat.cpp:1111:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress]
  cstat.cpp:1117:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 8)))’ and NULL [-Waddress]
  cstat.cpp:1123:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress]
  cstat.cpp:1131:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 8)))’ and NULL [-Waddress]
  cstat.cpp:1133:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress]
  cstat.cpp:1141:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 4)))’ and NULL [-Waddress]
  cstat.cpp:1143:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘<unknown>’ [-Wrestrict]
  seppel.cpp:484:19: warning: ‘void operator delete [](void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘str’ [-Wrestrict]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/casper.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 ... 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 loading without being on the library search path ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) asymmetryCheck.Rd:21: Lost braces
    21 |   \item{...}{Other arguments to be passed on to code{plot}}
       |                                                     ^
checkRd: (-1) qqnormGenomeWide.Rd:35: Lost braces
    35 |   \item{...}{Other arguments to be passed on to code{plot}}
       |                                                     ^
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/casper.Rcheck/00check.log’
for details.