* using log directory 'd:/RCompile/CRANincoming/R-devel/hictkR.Rcheck'
* using R Under development (unstable) (2025-08-24 r88696 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'hictkR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'hictkR' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Roberto Rossini <roberros@uio.no>'

New submission

Possibly misspelled words in DESCRIPTION:
  hic (3:48, 17:63)
  mcool (17:51)

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: https://github.com/paulsengroup/hictkR/blob/main/tools/conanfile.py
    From: README.md
    Status: 404
    Message: Not Found
  URL: https://github.com/paulsengroup/hictkR/blob/main/tools/generate_makevars.py
    From: README.md
    Status: 404
    Message: Not Found

Size of tarball: 8526616 bytes
* 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 whether package 'hictkR' can be installed ... WARNING
Found the following significant warnings:
  D:/rtools45/x86_64-w64-mingw32.static.posix/include/psdk_inc/intrin-impl.h:838:1: warning: array subscript 0 is outside array bounds of 'long long unsigned int[0]' [-Warray-bounds=]
  D:/temp/2025_08_25_18_50_17_23135/RtmpEPRp0n/R.INSTALL308e022677fd3/hictkR/build/tmp/.conan2/p/b/arrowd58f5802aa538/b/src/cpp/src/arrow/vendored/portable-snippets/safe-math.h:171:9: warning: ISO C++ does not support '__int128' for 'psnip_safe_int128_t' [-Wpedantic]
  D:/temp/2025_08_25_18_50_17_23135/RtmpEPRp0n/R.INSTALL308e022677fd3/hictkR/build/tmp/.conan2/p/b/arrowd58f5802aa538/b/src/cpp/src/arrow/vendored/portable-snippets/safe-math.h:172:18: warning: ISO C++ does not support '__int128' for 'psnip_safe_uint128_t' [-Wpedantic]
  D:/temp/2025_08_25_18_50_17_23135/RtmpEPRp0n/R.INSTALL308e022677fd3/hictkR/build/tmp/.conan2/p/b/arrowd58f5802aa538/b/src/cpp/src/arrow/util/async_util.cc:466:78: warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
See 'd:/RCompile/CRANincoming/R-devel/hictkR.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking C++ specification ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 use of S3 registration ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... WARNING
File 'hictkR/libs/x64/hictkR.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Objects:
      '../build/tmp/.conan2/p/b/arrowd58f5802aa538/b/build/Release/release/libarrow.a',
      '../build/tmp/.conan2/p/b/arrowd58f5802aa538/p/lib/libarrow.a'
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects:
      '../build/tmp/.conan2/p/b/arrowd58f5802aa538/b/build/Release/release/libarrow.a',
      '../build/tmp/.conan2/p/b/arrowd58f5802aa538/p/lib/libarrow.a'
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
    Objects:
      '../build/tmp/.conan2/p/b/arrowd58f5802aa538/b/build/Release/release/libarrow.a',
      '../build/tmp/.conan2/p/b/arrowd58f5802aa538/p/lib/libarrow.a',
      '../build/tmp/.conan2/p/b/mimal1f2c33d951020/b/build/Release/libmimalloc-static.a',
      '../build/tmp/.conan2/p/b/mimal1f2c33d951020/p/lib/libmimalloc-static.a'

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE