* using log directory ‘/srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck’
* using R Under development (unstable) (2025-08-18 r88641)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* 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 ... [4s/6s] NOTE
Maintainer: ‘Roberto Rossini <roberros@uio.no>’

New submission

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

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
  URL: https://paulsengroup.github.io/hictkR (moved to https://paulsengroup.github.io/hictkR/)
    From: README.md
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

Size of tarball: 8527460 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hictkR’ can be installed ... [2196s/446s] WARNING
Found the following significant warnings:
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:574:5: warning: anonymous structs are a GNU extension [-Wgnu-anonymous-struct]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:578:5: warning: anonymous structs are a GNU extension [-Wgnu-anonymous-struct]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:582:5: warning: anonymous structs are a GNU extension [-Wgnu-anonymous-struct]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:586:5: warning: anonymous structs are a GNU extension [-Wgnu-anonymous-struct]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:574:5: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:578:5: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:582:5: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/regexp.h:586:5: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/prog.h:148:7: warning: anonymous structs are a GNU extension [-Wgnu-anonymous-struct]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/prog.h:148:7: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/prog.h:426:5: warning: anonymous structs are a GNU extension [-Wgnu-anonymous-struct]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/src/re2/prog.h:426:5: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/mimal99394af5d9006/b/src/src/options.c:266:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00_pkg_src/hictkR/scratch/tmp/.conan2/p/b/arrowb8a811625b276/b/src/cpp/src/arrow/util/async_util.cc:466:78: warning: passing no argument for the '...' parameter of a variadic macro is a C++20 extension [-Wc++20-extensions]
See ‘/srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck/00install.out’ for details.
Installation took CPU time 4.9 times elapsed time
* used C++ compiler: ‘Debian clang version 19.1.7 (3+b1)’
* checking C++ specification ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... WARNING
Found the following directory with the name of a check directory:
  ./scratch/tmp/.conan2/p/b/zstd070a39c42194c/b/build/Release/lib/CMakeFiles/libzstd_static.dir/srv/hornik/tmp/CRAN_pretest/hictkR.Rcheck
Most likely, these were included erroneously.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK
* checking Rd files ... [0s/0s] 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 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... WARNING
File ‘hictkR/libs/hictkR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects:
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/b/build/Release/release/libarrow.a’,
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/p/lib/libarrow.a’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects:
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/b/build/Release/release/libarrow.a’,
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/p/lib/libarrow.a’
  Found ‘abort’, possibly from ‘abort’ (C)
    Objects:
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/b/build/Release/release/libarrow.a’,
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/p/lib/libarrow.a’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/b/build/Release/src/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/p/lib/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/mimal99394af5d9006/b/build/Release/libmimalloc.a’,
      ‘../scratch/tmp/.conan2/p/b/mimal99394af5d9006/p/lib/libmimalloc.a’,
      ‘../scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/build/Release/libre2.a’,
      ‘../scratch/tmp/.conan2/p/b/re29b144cd95c60a/p/lib/libre2.a’
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects:
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/b/build/Release/src/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/p/lib/libhdf5.a’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects:
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/b/build/Release/src/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/p/lib/libhdf5.a’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects:
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/b/build/Release/release/libarrow.a’,
      ‘../scratch/tmp/.conan2/p/b/arrowb8a811625b276/p/lib/libarrow.a’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/b/build/Release/src/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/p/lib/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/mimal99394af5d9006/b/build/Release/libmimalloc.a’,
      ‘../scratch/tmp/.conan2/p/b/mimal99394af5d9006/p/lib/libmimalloc.a’,
      ‘../scratch/tmp/.conan2/p/b/re29b144cd95c60a/b/build/Release/libre2.a’,
      ‘../scratch/tmp/.conan2/p/b/re29b144cd95c60a/p/lib/libre2.a’,
      ‘../scratch/tmp/.conan2/p/b/zstd070a39c42194c/b/build/Release/lib/libzstd.a’,
      ‘../scratch/tmp/.conan2/p/b/zstd070a39c42194c/p/lib/libzstd.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Objects: ‘hictkr.o’, ‘hictkr_file.o’,
      ‘hictkr_multi_resolution_file.o’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/b/build/Release/src/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/hdf55c631f7ba4b81/p/lib/libhdf5.a’,
      ‘../scratch/tmp/.conan2/p/b/mimal99394af5d9006/b/build/Release/libmimalloc.a’,
      ‘../scratch/tmp/.conan2/p/b/mimal99394af5d9006/p/lib/libmimalloc.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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] OK
  Running ‘testthat.R’ [2s/2s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [3s/3s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 WARNINGs, 1 NOTE