* using log directory ‘/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck’ * using R Under development (unstable) (2025-10-22 r88967) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (7) Debian flang-new version 19.1.7 (7) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘hdf5lib/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hdf5lib’ version ‘1.14.6.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Daniel P. Smith ’ New submission Size of tarball: 17846558 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 ‘hdf5lib’ can be installed ... [151s/148s] OK * used C compiler: ‘Debian clang version 19.1.7 (7)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘cran-comments.md’ * 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 ... [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 ... [2s/2s] 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 ... NOTE Found the following sources/headers with CR or CRLF line endings: src/hdf5-1.14.6/hl/src/H5LTanalyze.c src/hdf5-1.14.6/hl/src/H5LTparse.c src/hdf5-1.14.6/src/H5Shyper.c src/zlib-1.3.1/zconf.h Some Unix compilers require LF line endings. * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: src/hdf5-1.14.6/bin/Makefile.in src/hdf5-1.14.6/c++/Makefile.in src/hdf5-1.14.6/c++/src/Makefile.in src/hdf5-1.14.6/c++/test/Makefile.in src/hdf5-1.14.6/fortran/Makefile.in src/hdf5-1.14.6/fortran/src/Makefile.in src/hdf5-1.14.6/fortran/test/Makefile src/hdf5-1.14.6/fortran/test/Makefile.in src/hdf5-1.14.6/fortran/testpar/Makefile.in src/hdf5-1.14.6/hl/Makefile.in src/hdf5-1.14.6/hl/c++/Makefile.in src/hdf5-1.14.6/hl/c++/examples/Makefile.in src/hdf5-1.14.6/hl/c++/src/Makefile.in src/hdf5-1.14.6/hl/c++/test/Makefile.in src/hdf5-1.14.6/hl/examples/Makefile.in src/hdf5-1.14.6/hl/fortran/Makefile.in src/hdf5-1.14.6/hl/fortran/examples/Makefile.in src/hdf5-1.14.6/hl/fortran/src/Makefile.in src/hdf5-1.14.6/hl/fortran/test/Makefile src/hdf5-1.14.6/hl/fortran/test/Makefile.in src/hdf5-1.14.6/hl/src/Makefile.in src/hdf5-1.14.6/hl/test/Makefile.in src/hdf5-1.14.6/hl/tools/Makefile.in src/hdf5-1.14.6/hl/tools/gif2h5/Makefile.in src/hdf5-1.14.6/hl/tools/h5watch/Makefile.in src/hdf5-1.14.6/java/Makefile.in src/hdf5-1.14.6/java/src/jni/Makefile.in src/hdf5-1.14.6/java/test/Makefile.in src/hdf5-1.14.6/src/Makefile.in src/hdf5-1.14.6/test/Makefile.in src/hdf5-1.14.6/testpar/Makefile.in src/hdf5-1.14.6/tools/Makefile.in src/hdf5-1.14.6/tools/lib/Makefile.in src/hdf5-1.14.6/tools/libtest/Makefile.in src/hdf5-1.14.6/tools/src/Makefile.in src/hdf5-1.14.6/tools/src/h5copy/Makefile.in src/hdf5-1.14.6/tools/src/h5diff/Makefile.in src/hdf5-1.14.6/tools/src/h5dump/Makefile.in src/hdf5-1.14.6/tools/src/h5format_convert/Makefile.in src/hdf5-1.14.6/tools/src/h5import/Makefile.in src/hdf5-1.14.6/tools/src/h5jam/Makefile.in src/hdf5-1.14.6/tools/src/h5ls/Makefile.in src/hdf5-1.14.6/tools/src/h5perf/Makefile.in src/hdf5-1.14.6/tools/src/h5repack/Makefile.in src/hdf5-1.14.6/tools/src/h5stat/Makefile.in src/hdf5-1.14.6/tools/src/misc/Makefile.in src/hdf5-1.14.6/tools/test/Makefile.in src/hdf5-1.14.6/tools/test/h5copy/Makefile.in src/hdf5-1.14.6/tools/test/h5diff/Makefile.in src/hdf5-1.14.6/tools/test/h5dump/Makefile.in src/hdf5-1.14.6/tools/test/h5format_convert/Makefile.in src/hdf5-1.14.6/tools/test/h5import/Makefile.in src/hdf5-1.14.6/tools/test/h5jam/Makefile.in src/hdf5-1.14.6/tools/test/h5ls/Makefile.in src/hdf5-1.14.6/tools/test/h5repack/Makefile.in src/hdf5-1.14.6/tools/test/h5stat/Makefile.in src/hdf5-1.14.6/tools/test/misc/Makefile.in src/hdf5-1.14.6/tools/test/misc/vds/Makefile.in src/hdf5-1.14.6/tools/test/perform/Makefile.in src/hdf5-1.14.6/utils/Makefile.in src/hdf5-1.14.6/utils/mirror_vfd/Makefile.in src/hdf5-1.14.6/utils/test/Makefile.in src/hdf5-1.14.6/utils/tools/Makefile.in src/hdf5-1.14.6/utils/tools/h5dwalk/Makefile.in src/hdf5-1.14.6/utils/tools/test/Makefile.in src/hdf5-1.14.6/utils/tools/test/h5dwalk/Makefile.in Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * 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 include directives in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... WARNING File ‘hdf5lib/libs/hdf5lib.so’: Found ‘abort’, possibly from ‘abort’ (C) Object: ‘hdf5-1.14.6/src/.libs/libhdf5.a’ Found ‘exit’, possibly from ‘exit’ (C) Object: ‘hdf5-1.14.6/hl/src/.libs/libhdf5_hl.a’ Found ‘printf’, possibly from ‘printf’ (C) Objects: ‘hdf5-1.14.6/hl/src/.libs/libhdf5_hl.a’, ‘hdf5-1.14.6/src/.libs/libhdf5.a’ Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Object: ‘hdf5-1.14.6/src/.libs/libhdf5.a’ Found ‘rand_r’, possibly from ‘rand_r’ (C) Object: ‘hdf5-1.14.6/src/.libs/libhdf5.a’ Found ‘stderr’, possibly from ‘stderr’ (C) Objects: ‘hdf5-1.14.6/hl/src/.libs/libhdf5_hl.a’, ‘hdf5-1.14.6/src/.libs/libhdf5.a’ Found ‘stdout’, possibly from ‘stdout’ (C) Objects: ‘hdf5-1.14.6/hl/src/.libs/libhdf5_hl.a’, ‘hdf5-1.14.6/src/.libs/libhdf5.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 examples ... NONE * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 WARNINGs, 3 NOTEs