this derivation will be built: /nix/store/30an0gpnh607njc6hnf2bz86p1b973l7-ViennaRNA-2.5.1.drv these 8 paths will be fetched (47.5 MiB download, 200.6 MiB unpacked): /nix/store/sxdx80lmk4zkhb51f4x5dgqvxgmx55wl-gcc-11.3.0 /nix/store/wn31i3dzwahz6ccws8bs1nwyqrpgsvj7-gcc-wrapper-11.3.0 /nix/store/4n2j62ghfgsk5amycf3zss01b3wp0846-gmp-with-cxx-6.2.1 /nix/store/00wr31rqp81c21is5vxij5146bcm8slq-gmp-with-cxx-6.2.1-dev /nix/store/5p78v8ly9s5063jbp9j5bk0g5mj6s3gr-gsl-2.7.1 /nix/store/1pn7w5hbjqnlx2zq0sa6yzr7nckf9q8m-mpfr-4.1.1 /nix/store/g95dh9mhz816izca6zhvi5z6gjscf4cb-mpfr-4.1.1-dev /nix/store/cp65c8nk29qq5cl1wyy5qyw103cwmax7-stdenv-linux building '/nix/store/30an0gpnh607njc6hnf2bz86p1b973l7-ViennaRNA-2.5.1.drv' ViennaRNA-2.5.1> unpacking sources ViennaRNA-2.5.1> unpacking source archive /nix/store/mxbfkn8wrd1g1qpifs1s2c3knhrgrc9v-ViennaRNA-2.5.1.tar.gz ViennaRNA-2.5.1> source root is ViennaRNA-2.5.1 ViennaRNA-2.5.1> setting SOURCE_DATE_EPOCH to timestamp 1654156553 of file ViennaRNA-2.5.1/src/RNAforester/g2-0.72/src/g2_virtual_device.h ViennaRNA-2.5.1> patching sources ViennaRNA-2.5.1> configuring ViennaRNA-2.5.1> fixing libtool script ./config/ltmain.sh ViennaRNA-2.5.1> ./configure ViennaRNA-2.5.1> configure flags: --disable-static --disable-dependency-tracking --prefix=/nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1 --with-cluster --with-kinwalker ViennaRNA-2.5.1> checking for gcc... gcc ViennaRNA-2.5.1> checking whether the C compiler works... yes ViennaRNA-2.5.1> checking for C compiler default output file name... a.out ViennaRNA-2.5.1> checking for suffix of executables... ViennaRNA-2.5.1> checking whether we are cross compiling... no ViennaRNA-2.5.1> checking for suffix of object files... o ViennaRNA-2.5.1> checking whether the compiler supports GNU C... yes ViennaRNA-2.5.1> checking whether gcc accepts -g... yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... none needed ViennaRNA-2.5.1> checking whether gcc understands -c and -o together... yes ViennaRNA-2.5.1> checking for stdio.h... yes ViennaRNA-2.5.1> checking for stdlib.h... yes ViennaRNA-2.5.1> checking for string.h... yes ViennaRNA-2.5.1> checking for inttypes.h... yes ViennaRNA-2.5.1> checking for stdint.h... yes ViennaRNA-2.5.1> checking for strings.h... yes ViennaRNA-2.5.1> checking for sys/stat.h... yes ViennaRNA-2.5.1> checking for sys/types.h... yes ViennaRNA-2.5.1> checking for unistd.h... yes ViennaRNA-2.5.1> checking for wchar.h... yes ViennaRNA-2.5.1> checking for minix/config.h... no ViennaRNA-2.5.1> checking whether it is safe to define __EXTENSIONS__... yes ViennaRNA-2.5.1> checking whether _XOPEN_SOURCE should be defined... no ViennaRNA-2.5.1> checking whether make supports nested variables... yes ViennaRNA-2.5.1> checking for a BSD-compatible install... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/install -c ViennaRNA-2.5.1> checking whether build environment is sane... yes ViennaRNA-2.5.1> checking for a race-free mkdir -p... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/mkdir -p ViennaRNA-2.5.1> checking for gawk... gawk ViennaRNA-2.5.1> checking whether make sets $(MAKE)... yes ViennaRNA-2.5.1> checking whether make supports the include directive... yes (GNU style) ViennaRNA-2.5.1> checking whether UID '1000' is supported by ustar format... yes ViennaRNA-2.5.1> checking whether GID '100' is supported by ustar format... yes ViennaRNA-2.5.1> checking how to create a ustar tar archive... gnutar ViennaRNA-2.5.1> checking dependency style of gcc... none ViennaRNA-2.5.1> checking if malloc debugging is wanted... no ViennaRNA-2.5.1> checking build system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking host system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking whether the compiler supports GNU C++... yes ViennaRNA-2.5.1> checking whether g++ accepts -g... yes ViennaRNA-2.5.1> checking for g++ option to enable C++11 features... none needed ViennaRNA-2.5.1> checking dependency style of g++... none ViennaRNA-2.5.1> checking how to run the C++ preprocessor... g++ -E ViennaRNA-2.5.1> checking for gcc... (cached) gcc ViennaRNA-2.5.1> checking whether the compiler supports GNU C... (cached) yes ViennaRNA-2.5.1> checking whether gcc accepts -g... (cached) yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... (cached) none needed ViennaRNA-2.5.1> checking whether gcc understands -c and -o together... (cached) yes ViennaRNA-2.5.1> checking how to run the C preprocessor... gcc -E ViennaRNA-2.5.1> checking the archiver (ar) interface... ar ViennaRNA-2.5.1> checking whether make sets $(MAKE)... (cached) yes ViennaRNA-2.5.1> checking for grep that handles long lines and -e... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep ViennaRNA-2.5.1> checking for a sed that does not truncate output... /nix/store/5dv5cq1lwvsijr9p16p2kp79g1dbajk3-gnused-4.8/bin/sed ViennaRNA-2.5.1> checking for gawk... (cached) gawk ViennaRNA-2.5.1> checking whether ln -s works... yes ViennaRNA-2.5.1> checking how to print strings... printf ViennaRNA-2.5.1> checking for a sed that does not truncate output... (cached) /nix/store/5dv5cq1lwvsijr9p16p2kp79g1dbajk3-gnused-4.8/bin/sed ViennaRNA-2.5.1> checking for egrep... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep -E ViennaRNA-2.5.1> checking for fgrep... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep -F ViennaRNA-2.5.1> checking for ld used by gcc... ld ViennaRNA-2.5.1> checking if the linker (ld) is GNU ld... yes ViennaRNA-2.5.1> checking for BSD- or MS-compatible name lister (nm)... nm ViennaRNA-2.5.1> checking the name lister (nm) interface... BSD nm ViennaRNA-2.5.1> checking the maximum length of command line arguments... 1572864 ViennaRNA-2.5.1> checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop ViennaRNA-2.5.1> checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop ViennaRNA-2.5.1> checking for ld option to reload object files... -r ViennaRNA-2.5.1> checking for file... file ViennaRNA-2.5.1> checking for objdump... objdump ViennaRNA-2.5.1> checking how to recognize dependent libraries... (cached) pass_all ViennaRNA-2.5.1> checking for dlltool... no ViennaRNA-2.5.1> checking how to associate runtime and link libraries... printf %s\n ViennaRNA-2.5.1> checking for archiver @FILE support... @ ViennaRNA-2.5.1> checking for strip... strip ViennaRNA-2.5.1> checking for ranlib... ranlib ViennaRNA-2.5.1> checking command to parse nm output from gcc object... ok ViennaRNA-2.5.1> checking for sysroot... no ViennaRNA-2.5.1> checking for a working dd... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/dd ViennaRNA-2.5.1> checking how to truncate binary pipes... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/dd bs=4096 count=1 ViennaRNA-2.5.1> checking for mt... no ViennaRNA-2.5.1> checking if : is a manifest tool... no ViennaRNA-2.5.1> checking for dlfcn.h... yes ViennaRNA-2.5.1> checking for objdir... .libs ViennaRNA-2.5.1> checking if gcc supports -fno-rtti -fno-exceptions... no ViennaRNA-2.5.1> checking for gcc option to produce PIC... -fPIC -DPIC ViennaRNA-2.5.1> checking if gcc PIC flag -fPIC -DPIC works... yes ViennaRNA-2.5.1> checking if gcc static flag -static works... no ViennaRNA-2.5.1> checking if gcc supports -c -o file.o... yes ViennaRNA-2.5.1> checking if gcc supports -c -o file.o... (cached) yes ViennaRNA-2.5.1> checking whether the gcc linker (ld -m elf_x86_64) supports shared libraries... yes ViennaRNA-2.5.1> checking whether -lc should be explicitly linked in... no ViennaRNA-2.5.1> checking dynamic linker characteristics... GNU/Linux ld.so ViennaRNA-2.5.1> checking how to hardcode library paths into programs... immediate ViennaRNA-2.5.1> checking whether stripping libraries is possible... yes ViennaRNA-2.5.1> checking if libtool supports shared libraries... yes ViennaRNA-2.5.1> checking whether to build shared libraries... yes ViennaRNA-2.5.1> checking whether to build static libraries... no ViennaRNA-2.5.1> checking how to run the C++ preprocessor... g++ -E ViennaRNA-2.5.1> checking for ld used by g++... ld -m elf_x86_64 ViennaRNA-2.5.1> checking if the linker (ld -m elf_x86_64) is GNU ld... yes ViennaRNA-2.5.1> checking whether the g++ linker (ld -m elf_x86_64) supports shared libraries... yes ViennaRNA-2.5.1> checking for g++ option to produce PIC... -fPIC -DPIC ViennaRNA-2.5.1> checking if g++ PIC flag -fPIC -DPIC works... yes ViennaRNA-2.5.1> checking if g++ static flag -static works... no ViennaRNA-2.5.1> checking if g++ supports -c -o file.o... yes ViennaRNA-2.5.1> checking if g++ supports -c -o file.o... (cached) yes ViennaRNA-2.5.1> checking whether the g++ linker (ld -m elf_x86_64) supports shared libraries... yes ViennaRNA-2.5.1> checking dynamic linker characteristics... (cached) GNU/Linux ld.so ViennaRNA-2.5.1> checking how to hardcode library paths into programs... immediate ViennaRNA-2.5.1> checking for exp in -lm... yes ViennaRNA-2.5.1> ./configure: line 19107: #include: command not found ViennaRNA-2.5.1> checking for egrep... (cached) /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep -E ViennaRNA-2.5.1> checking for _Bool... yes ViennaRNA-2.5.1> checking for stdbool.h that conforms to C99... yes ViennaRNA-2.5.1> checking for malloc.h... yes ViennaRNA-2.5.1> checking for float.h... yes ViennaRNA-2.5.1> checking for limits.h... yes ViennaRNA-2.5.1> checking for stdlib.h... (cached) yes ViennaRNA-2.5.1> checking for string.h... (cached) yes ViennaRNA-2.5.1> checking for strings.h... (cached) yes ViennaRNA-2.5.1> checking for unistd.h... (cached) yes ViennaRNA-2.5.1> checking for math.h... yes ViennaRNA-2.5.1> checking for stdarg.h... yes ViennaRNA-2.5.1> checking for GNU libc compatible malloc... yes ViennaRNA-2.5.1> checking for GNU libc compatible realloc... yes ViennaRNA-2.5.1> checking for working strtod... yes ViennaRNA-2.5.1> checking for floor... yes ViennaRNA-2.5.1> checking for strdup... yes ViennaRNA-2.5.1> checking for strstr... yes ViennaRNA-2.5.1> checking for strchr... yes ViennaRNA-2.5.1> checking for strrchr... yes ViennaRNA-2.5.1> checking for strstr... (cached) yes ViennaRNA-2.5.1> checking for strtol... yes ViennaRNA-2.5.1> checking for strtoul... yes ViennaRNA-2.5.1> checking for pow... yes ViennaRNA-2.5.1> checking for rint... yes ViennaRNA-2.5.1> checking for sqrt... yes ViennaRNA-2.5.1> checking for erand48... yes ViennaRNA-2.5.1> checking for memset... yes ViennaRNA-2.5.1> checking for memmove... yes ViennaRNA-2.5.1> checking for erand48... (cached) yes ViennaRNA-2.5.1> checking for asprintf... yes ViennaRNA-2.5.1> checking for vasprintf... yes ViennaRNA-2.5.1> checking for an ANSI C-conforming const... yes ViennaRNA-2.5.1> checking for size_t... yes ViennaRNA-2.5.1> checking for inline... inline ViennaRNA-2.5.1> checking for pdflatex... no ViennaRNA-2.5.1> checking for bibtex... no ViennaRNA-2.5.1> checking for makeindex... no ViennaRNA-2.5.1> checking for pkg-config... no ViennaRNA-2.5.1> checking for C compiler vendor... gnu ViennaRNA-2.5.1> checking for perl... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/bin/perl ViennaRNA-2.5.1> checking whether C compiler accepts -fno-strict-aliasing... yes ViennaRNA-2.5.1> checking whether C++ compiler accepts -fno-strict-aliasing... yes ViennaRNA-2.5.1> checking whether the linker accepts -fno-strict-aliasing... yes ViennaRNA-2.5.1> checking whether the C compiler allows unnamed unions of unnamed structs... yes ViennaRNA-2.5.1> checking whether the C++ compiler allows unnamed unions of unnamed structs... yes ViennaRNA-2.5.1> checking whether C compiler accepts -flto... yes ViennaRNA-2.5.1> checking whether C++ compiler accepts -flto... yes ViennaRNA-2.5.1> checking whether C compiler accepts -ffat-lto-objects... yes ViennaRNA-2.5.1> checking whether C++ compiler accepts -ffat-lto-objects... yes ViennaRNA-2.5.1> configure: WARNING: Trying to re-set ar/ranlib/nm to compiler specific wrappers ViennaRNA-2.5.1> checking for gcc-ar... gcc-ar ViennaRNA-2.5.1> checking for gcc-ranlib... gcc-ranlib ViennaRNA-2.5.1> checking for gcc-nm... gcc-nm ViennaRNA-2.5.1> checking whether the linker supports Link time Optimization (LTO)... yes ViennaRNA-2.5.1> checking for ./src/libsvm-3.25/svm.cpp... yes ViennaRNA-2.5.1> checking for ./src/libsvm-3.25/svm.h... yes ViennaRNA-2.5.1> checking for ./src/json/json.c... yes ViennaRNA-2.5.1> checking for ./src/json/json.h... yes ViennaRNA-2.5.1> checking for cblas_dgemm in -lgslcblas... yes ViennaRNA-2.5.1> checking for gsl_blas_dgemm in -lgsl... yes ViennaRNA-2.5.1> checking for OpenMP flag of C compiler... -fopenmp ViennaRNA-2.5.1> checking for OpenMP flag of C++ compiler... -fopenmp ViennaRNA-2.5.1> checking whether gcc is Clang... no ViennaRNA-2.5.1> checking whether pthreads work with "-pthread" and "-lpthread"... yes ViennaRNA-2.5.1> checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE ViennaRNA-2.5.1> checking whether more special flags are required for pthreads... no ViennaRNA-2.5.1> checking for PTHREAD_PRIO_INHERIT... yes ViennaRNA-2.5.1> checking compiler support for AVX 512 instructions... yes ViennaRNA-2.5.1> checking compiler support for SSE 4.1 instructions... yes ViennaRNA-2.5.1> checking whether C compiler accepts -ftree-vectorize... yes ViennaRNA-2.5.1> checking for mpfr.h... yes ViennaRNA-2.5.1> checking whether we can compile programs with mpfr support... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/plotting/naview/naview.c... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/plotting/naview/naview.h... yes ViennaRNA-2.5.1> checking for ./interfaces/Makefile.am... yes ViennaRNA-2.5.1> checking for swig... no ViennaRNA-2.5.1> checking for swig2.0... no ViennaRNA-2.5.1> checking for ./interfaces/Perl/Makefile.am... yes ViennaRNA-2.5.1> checking for ./interfaces/Perl/RNA_wrap.cpp... yes ViennaRNA-2.5.1> checking for ./interfaces/Perl/RNA.pm... yes ViennaRNA-2.5.1> checking for /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/bin/perl... (cached) /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/bin/perl ViennaRNA-2.5.1> checking for Perl prefix... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0 ViennaRNA-2.5.1> checking for Perl siteprefix... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0 ViennaRNA-2.5.1> checking for Perl vendorprefix... ViennaRNA-2.5.1> checking for Perl extension include path... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/lib/perl5/5.36.0/x86_64-linux-thread-multi/CORE ViennaRNA-2.5.1> checking for Perl extension target directory... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/lib/perl5/site_perl/5.36.0/x86_64-linux-thread-multi ViennaRNA-2.5.1> checking for architecture dependent Perl extension site target directory... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/lib/perl5/site_perl/5.36.0/x86_64-linux-thread-multi ViennaRNA-2.5.1> checking for architecture dependent Perl extension vendor target directory... ViennaRNA-2.5.1> checking for architecture independent Perl extension site target directory... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/lib/perl5/site_perl/5.36.0 ViennaRNA-2.5.1> checking for architecture independent Perl extension vendor target directory... ViennaRNA-2.5.1> checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/no-such-path/include ViennaRNA-2.5.1> checking for Perl extensions linker flags... -shared -O2 -L/nix/store/ayfr5l52xkqqjn3n4h9jfacgnchz1z7s-glibc-2.35-224/lib -fstack-protector-strong ViennaRNA-2.5.1> checking for Perl dynamic library extension... .so ViennaRNA-2.5.1> checking for ./interfaces/Python2/Makefile.am... yes ViennaRNA-2.5.1> checking for ./interfaces/Python2/RNA_wrap.cpp... yes ViennaRNA-2.5.1> checking for ./interfaces/Python2/RNA.py... yes ViennaRNA-2.5.1> checking for python2... no ViennaRNA-2.5.1> checking for python2.7... no ViennaRNA-2.5.1> checking for python2.6... no ViennaRNA-2.5.1> checking for ./interfaces/Python/Makefile.am... yes ViennaRNA-2.5.1> checking for ./interfaces/Python/RNA_wrap.cpp... yes ViennaRNA-2.5.1> checking for ./interfaces/Python/RNA.py... yes ViennaRNA-2.5.1> checking for python3... /nix/store/al6g1zbk8li6p8mcyp0h60d08jaahf8c-python3-3.10.9/bin/python3 ViennaRNA-2.5.1> checking for Python3 include path... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives ViennaRNA-2.5.1> :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead ViennaRNA-2.5.1> /nix/store/al6g1zbk8li6p8mcyp0h60d08jaahf8c-python3-3.10.9/include/python3.10 ViennaRNA-2.5.1> checking for /nix/store/al6g1zbk8li6p8mcyp0h60d08jaahf8c-python3-3.10.9/include/python3.10/Python.h... yes ViennaRNA-2.5.1> checking for Python3 ldflags... ViennaRNA-2.5.1> checking for Python3 extension linker... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives ViennaRNA-2.5.1> :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead ViennaRNA-2.5.1> gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.2.13/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.5.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.2.9/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.4.4/lib -L/nix/store/vamwsqfpvgfwnc7ksa8k4aa52my5r1bq-libxcrypt-4.4.33/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.23/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.40.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.1p2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.3-p20220507/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.0.7/lib -L/nix/store/11mrj0y0k09j7pzcr78iy5fxgcmzjxq6-tzdata-2022g/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.2.13/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.5.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.2.9/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.4.4/lib -L/nix/store/vamwsqfpvgfwnc7ksa8k4aa52my5r1bq-libxcrypt-4.4.33/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.23/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.40.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.1p2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.3-p20220507/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.0.7/lib -L/nix/store/11mrj0y0k09j7pzcr78iy5fxgcmzjxq6-tzdata-2022g/lib ViennaRNA-2.5.1> checking for directory to install Python3 scripts in... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives ViennaRNA-2.5.1> :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead ViennaRNA-2.5.1> ${prefix}/lib/python3.10/site-packages ViennaRNA-2.5.1> checking for directory to install architecture dependent python3 things in... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives ViennaRNA-2.5.1> :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead ViennaRNA-2.5.1> ${exec_prefix}/lib/python3.10/site-packages ViennaRNA-2.5.1> checking for Python3 module extension... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives ViennaRNA-2.5.1> :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead ViennaRNA-2.5.1> .cpython-310-x86_64-linux-gnu.so ViennaRNA-2.5.1> checking for Python3 tag for cached compiled scripts... cpython-310 ViennaRNA-2.5.1> checking for Python3 extension of cached and optimized bytecode... cpython-310.opt-1.pyc ViennaRNA-2.5.1> checking for doxygen... no ViennaRNA-2.5.1> checking for dot... no ViennaRNA-2.5.1> checking for egrep... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/egrep ViennaRNA-2.5.1> checking for perl... /nix/store/n48i43wkly6kfhxz4ypcxbsv2pr7ggzh-perl-5.36.0/bin/perl ViennaRNA-2.5.1> checking for doc/RNAlib-2.5.1.pdf... yes ViennaRNA-2.5.1> checking for doc/html/index.html... yes ViennaRNA-2.5.1> checking for htlatex... no ViennaRNA-2.5.1> configure: WARNING: Could not find pdflatex! ViennaRNA-2.5.1> configure: WARNING: deactivating automatic (re)generation of tutorial! ViennaRNA-2.5.1> checking for RNA-Tutorial/RNA-tutorial-2.5.1.pdf... yes ViennaRNA-2.5.1> configure: WARNING: Could not find pdflatex! ViennaRNA-2.5.1> configure: WARNING: deactivating automatic (re)generation of CLA! ViennaRNA-2.5.1> checking for doc/CLA/ViennaRNA-CLA-Individual.pdf... yes ViennaRNA-2.5.1> checking for doc/CLA/ViennaRNA-CLA-Entity.pdf... yes ViennaRNA-2.5.1> checking for CHECK... no ViennaRNA-2.5.1> configure: WARNING: check not found -- will not build C-library Unit tests ViennaRNA-2.5.1> checking for diff... /nix/store/49y3r0gr9m6k20d91kl6dgp4b9a6m72v-diffutils-3.8/bin/diff ViennaRNA-2.5.1> checking for xxd... no ViennaRNA-2.5.1> checking for gengetopt... no ViennaRNA-2.5.1> checking for help2man... no ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/structure_plot_macro_base.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/structure_plot_macro_extras.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_base.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_turn.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_sd.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_ud.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_sc_motifs.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_linear_data.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/postscript/aln_macro_base.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/svg/structure_plot_header.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/svg/structure_plot_footer.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/misc/dna_mathews1999.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/misc/dna_mathews2004.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/misc/rna_andronescu2007.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/misc/rna_langdon2018.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/misc/rna_misc_special_hairpins.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/misc/rna_turner1999.hex... yes ViennaRNA-2.5.1> checking for ./src/ViennaRNA/static/misc/rna_turner2004.hex... yes ViennaRNA-2.5.1> checking whether g++ supports C++11 features with -std=c++11... yes ViennaRNA-2.5.1> checking for ./src/dlib-19.23/dlib/all/source.cpp... yes ViennaRNA-2.5.1> checking for ./src/Kinfold/Makefile.am... yes ViennaRNA-2.5.1> checking for ./src/RNAforester/Makefile.am... yes ViennaRNA-2.5.1> checking for ./src/Cluster/Makefile.am... yes ViennaRNA-2.5.1> checking for ./src/Kinwalker/Makefile.am... yes ViennaRNA-2.5.1> checking for ./src/RNAlocmin/Makefile.am... yes ViennaRNA-2.5.1> checking that generated files are newer than configure... done ViennaRNA-2.5.1> configure: creating ./config.status ViennaRNA-2.5.1> config.status: creating packaging/macosx/Makefile ViennaRNA-2.5.1> config.status: creating packaging/macosx/Distribution.xml ViennaRNA-2.5.1> config.status: creating packaging/macosx/resources/welcome.txt ViennaRNA-2.5.1> config.status: creating src/ViennaRNA/plotting/naview/Makefile ViennaRNA-2.5.1> config.status: creating interfaces/Perl/Makefile ViennaRNA-2.5.1> config.status: creating interfaces/Perl/version.i ViennaRNA-2.5.1> config.status: creating interfaces/Python/Makefile ViennaRNA-2.5.1> config.status: creating interfaces/Python/version.i ViennaRNA-2.5.1> config.status: creating tests/Makefile ViennaRNA-2.5.1> config.status: creating tests/RNApath.py ViennaRNA-2.5.1> config.status: creating tests/RNAHelpers.pm ViennaRNA-2.5.1> config.status: creating tests/test-env.sh ViennaRNA-2.5.1> config.status: creating src/ViennaRNA/static/templates_postscript.h ViennaRNA-2.5.1> config.status: creating src/ViennaRNA/static/templates_svg.h ViennaRNA-2.5.1> config.status: creating src/ViennaRNA/static/energy_parameter_sets.h ViennaRNA-2.5.1> config.status: creating src/Cluster/Makefile ViennaRNA-2.5.1> config.status: creating src/ViennaRNA/vrna_config.h ViennaRNA-2.5.1> config.status: creating misc/Makefile ViennaRNA-2.5.1> config.status: creating interfaces/Makefile ViennaRNA-2.5.1> config.status: creating Makefile ViennaRNA-2.5.1> config.status: creating RNAlib2.pc ViennaRNA-2.5.1> config.status: creating src/Utils/Makefile ViennaRNA-2.5.1> config.status: creating src/bin/Makefile ViennaRNA-2.5.1> config.status: creating src/Makefile ViennaRNA-2.5.1> config.status: creating src/ViennaRNA/Makefile ViennaRNA-2.5.1> config.status: creating src/ViennaRNA/static/Makefile ViennaRNA-2.5.1> config.status: creating man/Makefile ViennaRNA-2.5.1> config.status: creating doc/Makefile ViennaRNA-2.5.1> config.status: creating doc/CLA/Makefile ViennaRNA-2.5.1> config.status: creating RNA-Tutorial/Makefile ViennaRNA-2.5.1> config.status: creating man/cmdlopt.sh ViennaRNA-2.5.1> config.status: creating examples/Makefile ViennaRNA-2.5.1> config.status: creating packaging/viennarna.spec ViennaRNA-2.5.1> config.status: creating packaging/PKGBUILD ViennaRNA-2.5.1> config.status: creating packaging/win_installer_archlinux_i686.nsi ViennaRNA-2.5.1> config.status: creating packaging/win_installer_archlinux_x86_64.nsi ViennaRNA-2.5.1> config.status: creating packaging/win_installer_fedora_i686.nsi ViennaRNA-2.5.1> config.status: creating packaging/win_installer_fedora_x86_64.nsi ViennaRNA-2.5.1> config.status: creating config.h ViennaRNA-2.5.1> config.status: executing depfiles commands ViennaRNA-2.5.1> config.status: executing libtool commands ViennaRNA-2.5.1> === configuring in src/Kinfold (/build/ViennaRNA-2.5.1/src/Kinfold) ViennaRNA-2.5.1> configure: running /nix/store/4xw8n979xpivdc46a9ndcvyhwgif00hz-bash-5.1-p16/bin/bash ./configure --disable-option-checking '--prefix=/nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1' '--disable-static' '--disable-dependency-tracking' '--with-cluster' '--with-kinwalker' 'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. ViennaRNA-2.5.1> checking whether make supports nested variables... yes ViennaRNA-2.5.1> checking for a BSD-compatible install... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/install -c ViennaRNA-2.5.1> checking whether build environment is sane... yes ViennaRNA-2.5.1> checking for a race-free mkdir -p... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/mkdir -p ViennaRNA-2.5.1> checking for gawk... gawk ViennaRNA-2.5.1> checking whether make sets $(MAKE)... yes ViennaRNA-2.5.1> checking if malloc debugging is wanted... no ViennaRNA-2.5.1> checking for gcc... gcc ViennaRNA-2.5.1> checking whether the C compiler works... yes ViennaRNA-2.5.1> checking for C compiler default output file name... a.out ViennaRNA-2.5.1> checking for suffix of executables... ViennaRNA-2.5.1> checking whether we are cross compiling... no ViennaRNA-2.5.1> checking for suffix of object files... o ViennaRNA-2.5.1> checking whether the compiler supports GNU C... yes ViennaRNA-2.5.1> checking whether gcc accepts -g... yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... none needed ViennaRNA-2.5.1> checking whether gcc understands -c and -o together... yes ViennaRNA-2.5.1> checking whether make supports the include directive... yes (GNU style) ViennaRNA-2.5.1> checking dependency style of gcc... none ViennaRNA-2.5.1> checking build system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking host system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking for strdup... yes ViennaRNA-2.5.1> checking for memset... yes ViennaRNA-2.5.1> checking for strchr... yes ViennaRNA-2.5.1> checking for pkg-config... no ViennaRNA-2.5.1> checking for VRNA... yes ViennaRNA-2.5.1> checking for stdio.h... yes ViennaRNA-2.5.1> checking for stdlib.h... yes ViennaRNA-2.5.1> checking for string.h... yes ViennaRNA-2.5.1> checking for inttypes.h... yes ViennaRNA-2.5.1> checking for stdint.h... yes ViennaRNA-2.5.1> checking for strings.h... yes ViennaRNA-2.5.1> checking for sys/stat.h... yes ViennaRNA-2.5.1> checking for sys/types.h... yes ViennaRNA-2.5.1> checking for unistd.h... yes ViennaRNA-2.5.1> ./configure: line 4958: #include: command not found ViennaRNA-2.5.1> checking for grep that handles long lines and -e... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep ViennaRNA-2.5.1> checking for egrep... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep -E ViennaRNA-2.5.1> checking for stdlib.h... (cached) yes ViennaRNA-2.5.1> checking for string.h... (cached) yes ViennaRNA-2.5.1> checking for strings.h... (cached) yes ViennaRNA-2.5.1> checking for unistd.h... (cached) yes ViennaRNA-2.5.1> checking for exp in -lm... yes ViennaRNA-2.5.1> checking for an ANSI C-conforming const... yes ViennaRNA-2.5.1> checking that generated files are newer than configure... done ViennaRNA-2.5.1> configure: creating ./config.status ViennaRNA-2.5.1> config.status: creating Example/Makefile ViennaRNA-2.5.1> config.status: creating Makefile ViennaRNA-2.5.1> config.status: creating config.h ViennaRNA-2.5.1> config.status: executing depfiles commands ViennaRNA-2.5.1> === configuring in src/RNAforester (/build/ViennaRNA-2.5.1/src/RNAforester) ViennaRNA-2.5.1> configure: running /nix/store/4xw8n979xpivdc46a9ndcvyhwgif00hz-bash-5.1-p16/bin/bash ./configure --disable-option-checking '--prefix=/nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1' '--disable-static' '--disable-dependency-tracking' '--with-cluster' '--with-kinwalker' 'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. ViennaRNA-2.5.1> checking whether make supports nested variables... yes ViennaRNA-2.5.1> checking for a BSD-compatible install... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/install -c ViennaRNA-2.5.1> checking whether build environment is sane... yes ViennaRNA-2.5.1> checking for a race-free mkdir -p... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/mkdir -p ViennaRNA-2.5.1> checking for gawk... gawk ViennaRNA-2.5.1> checking whether make sets $(MAKE)... yes ViennaRNA-2.5.1> checking whether the C++ compiler works... yes ViennaRNA-2.5.1> checking for C++ compiler default output file name... a.out ViennaRNA-2.5.1> checking for suffix of executables... ViennaRNA-2.5.1> checking whether we are cross compiling... no ViennaRNA-2.5.1> checking for suffix of object files... o ViennaRNA-2.5.1> checking whether the compiler supports GNU C++... yes ViennaRNA-2.5.1> checking whether g++ accepts -g... yes ViennaRNA-2.5.1> checking for g++ option to enable C++11 features... none needed ViennaRNA-2.5.1> checking whether make supports the include directive... yes (GNU style) ViennaRNA-2.5.1> checking dependency style of g++... none ViennaRNA-2.5.1> checking for gcc... gcc ViennaRNA-2.5.1> checking whether the compiler supports GNU C... yes ViennaRNA-2.5.1> checking whether gcc accepts -g... yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... none needed ViennaRNA-2.5.1> checking whether gcc understands -c and -o together... yes ViennaRNA-2.5.1> checking dependency style of gcc... none ViennaRNA-2.5.1> checking for flex... no ViennaRNA-2.5.1> checking for lex... no ViennaRNA-2.5.1> checking for bison... no ViennaRNA-2.5.1> checking for byacc... no ViennaRNA-2.5.1> checking for g++ option to support OpenMP... -fopenmp ViennaRNA-2.5.1> checking for pkg-config... no ViennaRNA-2.5.1> checking for VRNA... yes ViennaRNA-2.5.1> checking for stdio.h... yes ViennaRNA-2.5.1> checking for stdlib.h... yes ViennaRNA-2.5.1> checking for string.h... yes ViennaRNA-2.5.1> checking for inttypes.h... yes ViennaRNA-2.5.1> checking for stdint.h... yes ViennaRNA-2.5.1> checking for strings.h... yes ViennaRNA-2.5.1> checking for sys/stat.h... yes ViennaRNA-2.5.1> checking for sys/types.h... yes ViennaRNA-2.5.1> checking for unistd.h... yes ViennaRNA-2.5.1> ./configure: line 5995: #include: command not found ViennaRNA-2.5.1> checking for grep that handles long lines and -e... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep ViennaRNA-2.5.1> checking for egrep... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep -E ViennaRNA-2.5.1> checking for g2.h... yes ViennaRNA-2.5.1> checking for an ANSI C-conforming const... yes ViennaRNA-2.5.1> checking for inline... inline ViennaRNA-2.5.1> checking for size_t... yes ViennaRNA-2.5.1> checking that generated files are newer than configure... done ViennaRNA-2.5.1> configure: creating ./config.status ViennaRNA-2.5.1> config.status: creating Makefile ViennaRNA-2.5.1> config.status: creating src/Makefile ViennaRNA-2.5.1> config.status: creating man/Makefile ViennaRNA-2.5.1> config.status: creating config.h ViennaRNA-2.5.1> config.status: executing depfiles commands ViennaRNA-2.5.1> === configuring in g2-0.72 (/build/ViennaRNA-2.5.1/src/RNAforester/g2-0.72) ViennaRNA-2.5.1> configure: running /nix/store/4xw8n979xpivdc46a9ndcvyhwgif00hz-bash-5.1-p16/bin/bash ./configure --disable-option-checking '--prefix=/nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1' '--disable-static' '--disable-dependency-tracking' '--with-cluster' '--with-kinwalker' 'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. ViennaRNA-2.5.1> checking build system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking host system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking for gcc... gcc ViennaRNA-2.5.1> checking whether the C compiler works... yes ViennaRNA-2.5.1> checking for C compiler default output file name... a.out ViennaRNA-2.5.1> checking for suffix of executables... ViennaRNA-2.5.1> checking whether we are cross compiling... no ViennaRNA-2.5.1> checking for suffix of object files... o ViennaRNA-2.5.1> checking whether the compiler supports GNU C... yes ViennaRNA-2.5.1> checking whether gcc accepts -g... yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... none needed ViennaRNA-2.5.1> checking how to run the C preprocessor... gcc -E ViennaRNA-2.5.1> checking whether the compiler supports GNU C++... yes ViennaRNA-2.5.1> checking whether g++ accepts -g... yes ViennaRNA-2.5.1> checking for g++ option to enable C++11 features... none needed ViennaRNA-2.5.1> checking for a BSD-compatible install... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/install -c ViennaRNA-2.5.1> checking for find... find ViennaRNA-2.5.1> checking for makedepend... : ViennaRNA-2.5.1> checking for dlopen in -ldl... yes ViennaRNA-2.5.1> checking for X... no ViennaRNA-2.5.1> checking for main in -lm... yes ViennaRNA-2.5.1> checking for main in -lX11... no ViennaRNA-2.5.1> checking for main in -lXext... no ViennaRNA-2.5.1> checking for main in -lgd... no ViennaRNA-2.5.1> checking for stdio.h... yes ViennaRNA-2.5.1> checking for stdlib.h... yes ViennaRNA-2.5.1> checking for string.h... yes ViennaRNA-2.5.1> checking for inttypes.h... yes ViennaRNA-2.5.1> checking for stdint.h... yes ViennaRNA-2.5.1> checking for strings.h... yes ViennaRNA-2.5.1> checking for sys/stat.h... yes ViennaRNA-2.5.1> checking for sys/types.h... yes ViennaRNA-2.5.1> checking for unistd.h... yes ViennaRNA-2.5.1> ./configure: line 5714: #include: command not found ViennaRNA-2.5.1> checking for grep that handles long lines and -e... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep ViennaRNA-2.5.1> checking for egrep... /nix/store/bcvccw6y9bfil6xrl5j7psza7hnd16ry-gnugrep-3.7/bin/grep -E ViennaRNA-2.5.1> checking for limits.h... yes ViennaRNA-2.5.1> ViennaRNA-2.5.1> configure: creating ./config.status ViennaRNA-2.5.1> config.status: creating Makefile ViennaRNA-2.5.1> config.status: creating demo/Makefile ViennaRNA-2.5.1> config.status: creating g2_perl/Makefile.PL ViennaRNA-2.5.1> config.status: creating g2_python/Makefile ViennaRNA-2.5.1> ViennaRNA-2.5.1> Supported devices: ViennaRNA-2.5.1> PostScript ViennaRNA-2.5.1> FIG ViennaRNA-2.5.1> ViennaRNA-2.5.1> Unsupported devices: ViennaRNA-2.5.1> X11 ViennaRNA-2.5.1> Xdbe ViennaRNA-2.5.1> Win32 ViennaRNA-2.5.1> GD ViennaRNA-2.5.1> GD (GIF) ViennaRNA-2.5.1> ViennaRNA-2.5.1> Run 'make depend' to create dependencies. ViennaRNA-2.5.1> ViennaRNA-2.5.1> === configuring in src/Kinwalker (/build/ViennaRNA-2.5.1/src/Kinwalker) ViennaRNA-2.5.1> configure: running /nix/store/4xw8n979xpivdc46a9ndcvyhwgif00hz-bash-5.1-p16/bin/bash ./configure --disable-option-checking '--prefix=/nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1' '--disable-static' '--disable-dependency-tracking' '--with-cluster' '--with-kinwalker' 'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. ViennaRNA-2.5.1> checking whether make supports nested variables... yes ViennaRNA-2.5.1> checking for a BSD-compatible install... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/install -c ViennaRNA-2.5.1> checking whether build environment is sane... yes ViennaRNA-2.5.1> checking for a race-free mkdir -p... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/mkdir -p ViennaRNA-2.5.1> checking for gawk... gawk ViennaRNA-2.5.1> checking whether make sets $(MAKE)... yes ViennaRNA-2.5.1> checking whether the C++ compiler works... yes ViennaRNA-2.5.1> checking for C++ compiler default output file name... a.out ViennaRNA-2.5.1> checking for suffix of executables... ViennaRNA-2.5.1> checking whether we are cross compiling... no ViennaRNA-2.5.1> checking for suffix of object files... o ViennaRNA-2.5.1> checking whether the compiler supports GNU C++... yes ViennaRNA-2.5.1> checking whether g++ accepts -g... yes ViennaRNA-2.5.1> checking for g++ option to enable C++11 features... none needed ViennaRNA-2.5.1> checking whether make supports the include directive... yes (GNU style) ViennaRNA-2.5.1> checking dependency style of g++... none ViennaRNA-2.5.1> checking for gcc... gcc ViennaRNA-2.5.1> checking whether the compiler supports GNU C... yes ViennaRNA-2.5.1> checking whether gcc accepts -g... yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... none needed ViennaRNA-2.5.1> checking whether gcc understands -c and -o together... yes ViennaRNA-2.5.1> checking dependency style of gcc... none ViennaRNA-2.5.1> checking for stdio.h... yes ViennaRNA-2.5.1> checking for stdlib.h... yes ViennaRNA-2.5.1> checking for string.h... yes ViennaRNA-2.5.1> checking for inttypes.h... yes ViennaRNA-2.5.1> checking for stdint.h... yes ViennaRNA-2.5.1> checking for strings.h... yes ViennaRNA-2.5.1> checking for sys/stat.h... yes ViennaRNA-2.5.1> checking for sys/types.h... yes ViennaRNA-2.5.1> checking for unistd.h... yes ViennaRNA-2.5.1> checking for malloc.h... yes ViennaRNA-2.5.1> checking for strings.h... (cached) yes ViennaRNA-2.5.1> checking for unistd.h... (cached) yes ViennaRNA-2.5.1> checking for inline... inline ViennaRNA-2.5.1> checking for pkg-config... no ViennaRNA-2.5.1> checking for VRNA... yes ViennaRNA-2.5.1> checking that generated files are newer than configure... done ViennaRNA-2.5.1> configure: creating ./config.status ViennaRNA-2.5.1> config.status: creating Makefile ViennaRNA-2.5.1> config.status: creating man/Makefile ViennaRNA-2.5.1> config.status: creating config.h ViennaRNA-2.5.1> config.status: executing depfiles commands ViennaRNA-2.5.1> === configuring in src/RNAlocmin (/build/ViennaRNA-2.5.1/src/RNAlocmin) ViennaRNA-2.5.1> configure: running /nix/store/4xw8n979xpivdc46a9ndcvyhwgif00hz-bash-5.1-p16/bin/bash ./configure --disable-option-checking '--prefix=/nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1' '--disable-static' '--disable-dependency-tracking' '--with-cluster' '--with-kinwalker' 'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. ViennaRNA-2.5.1> checking for gcc... gcc ViennaRNA-2.5.1> checking whether the C compiler works... yes ViennaRNA-2.5.1> checking for C compiler default output file name... a.out ViennaRNA-2.5.1> checking for suffix of executables... ViennaRNA-2.5.1> checking whether we are cross compiling... no ViennaRNA-2.5.1> checking for suffix of object files... o ViennaRNA-2.5.1> checking whether the compiler supports GNU C... yes ViennaRNA-2.5.1> checking whether gcc accepts -g... yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... none needed ViennaRNA-2.5.1> checking whether gcc understands -c and -o together... yes ViennaRNA-2.5.1> checking for stdio.h... yes ViennaRNA-2.5.1> checking for stdlib.h... yes ViennaRNA-2.5.1> checking for string.h... yes ViennaRNA-2.5.1> checking for inttypes.h... yes ViennaRNA-2.5.1> checking for stdint.h... yes ViennaRNA-2.5.1> checking for strings.h... yes ViennaRNA-2.5.1> checking for sys/stat.h... yes ViennaRNA-2.5.1> checking for sys/types.h... yes ViennaRNA-2.5.1> checking for unistd.h... yes ViennaRNA-2.5.1> checking for wchar.h... yes ViennaRNA-2.5.1> checking for minix/config.h... no ViennaRNA-2.5.1> checking whether it is safe to define __EXTENSIONS__... yes ViennaRNA-2.5.1> checking whether _XOPEN_SOURCE should be defined... no ViennaRNA-2.5.1> checking whether make supports nested variables... yes ViennaRNA-2.5.1> checking for a BSD-compatible install... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/install -c ViennaRNA-2.5.1> checking whether build environment is sane... yes ViennaRNA-2.5.1> checking for a race-free mkdir -p... /nix/store/h8gvq6r4hgpa71h44dmg9qfx03mj81sv-coreutils-9.1/bin/mkdir -p ViennaRNA-2.5.1> checking for gawk... gawk ViennaRNA-2.5.1> checking whether make sets $(MAKE)... yes ViennaRNA-2.5.1> checking whether make supports the include directive... yes (GNU style) ViennaRNA-2.5.1> checking dependency style of gcc... none ViennaRNA-2.5.1> checking build system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking host system type... x86_64-pc-linux-gnu ViennaRNA-2.5.1> checking whether the compiler supports GNU C++... yes ViennaRNA-2.5.1> checking whether g++ accepts -g... yes ViennaRNA-2.5.1> checking for g++ option to enable C++11 features... none needed ViennaRNA-2.5.1> checking dependency style of g++... none ViennaRNA-2.5.1> checking how to run the C++ preprocessor... g++ -E ViennaRNA-2.5.1> checking for gcc... (cached) gcc ViennaRNA-2.5.1> checking whether the compiler supports GNU C... (cached) yes ViennaRNA-2.5.1> checking whether gcc accepts -g... (cached) yes ViennaRNA-2.5.1> checking for gcc option to enable C11 features... (cached) none needed ViennaRNA-2.5.1> checking whether gcc understands -c and -o together... (cached) yes ViennaRNA-2.5.1> checking how to run the C preprocessor... gcc -E ViennaRNA-2.5.1> checking whether g++ supports C++11 features by default... yes ViennaRNA-2.5.1> checking for strchr... yes ViennaRNA-2.5.1> checking for strdup... yes ViennaRNA-2.5.1> checking for strtol... yes ViennaRNA-2.5.1> checking for limits.h... yes ViennaRNA-2.5.1> checking for _Bool... yes ViennaRNA-2.5.1> checking for stdbool.h that conforms to C99... yes ViennaRNA-2.5.1> checking for inline... inline ViennaRNA-2.5.1> checking for GNU libc compatible malloc... yes ViennaRNA-2.5.1> checking for GNU libc compatible realloc... yes ViennaRNA-2.5.1> checking for working strtod... yes ViennaRNA-2.5.1> checking for size_t... yes ViennaRNA-2.5.1> checking for pkg-config... no ViennaRNA-2.5.1> checking for VRNA... yes ViennaRNA-2.5.1> checking that generated files are newer than configure... done ViennaRNA-2.5.1> configure: creating ./config.status ViennaRNA-2.5.1> config.status: creating Makefile ViennaRNA-2.5.1> config.status: creating config.h ViennaRNA-2.5.1> config.status: executing depfiles commands ViennaRNA-2.5.1> configure: ViennaRNA-2.5.1> ViennaRNA-2.5.1> ====================================== ViennaRNA-2.5.1> ViennaRNA Package 2.5.1 ViennaRNA-2.5.1> ====================================== ViennaRNA-2.5.1> ViennaRNA-2.5.1> Successfully configured with the following options: ViennaRNA-2.5.1> ViennaRNA-2.5.1> Sub Packages ViennaRNA-2.5.1> ------------ ViennaRNA-2.5.1> * Kinfold : yes ViennaRNA-2.5.1> * RNAforester : yes ViennaRNA-2.5.1> * Analyse{Dists,Seqs} : yes ViennaRNA-2.5.1> * RNAlocmin : yes ViennaRNA-2.5.1> * Kinwalker : yes ViennaRNA-2.5.1> ViennaRNA-2.5.1> Extra Libraries ViennaRNA-2.5.1> --------------- ViennaRNA-2.5.1> * Support Vector Machine : yes ViennaRNA-2.5.1> * GNU Scientific Library : yes ViennaRNA-2.5.1> * GNU MPFR : yes ViennaRNA-2.5.1> * JSON : yes ViennaRNA-2.5.1> ViennaRNA-2.5.1> Features ViennaRNA-2.5.1> -------- ViennaRNA-2.5.1> * Use hash for NR Sampling : no ViennaRNA-2.5.1> * C11 features : yes ViennaRNA-2.5.1> * TTY colors : yes ViennaRNA-2.5.1> * Float Precision(PF} : no ViennaRNA-2.5.1> * Deprecation Warnings : no ViennaRNA-2.5.1> ViennaRNA-2.5.1> Optimizations ViennaRNA-2.5.1> ------------- ViennaRNA-2.5.1> * Auto Vectorization : yes ViennaRNA-2.5.1> * Explicit SIMD Extension : yes ViennaRNA-2.5.1> * Link Time Optimization : yes ViennaRNA-2.5.1> * POSIX Threads : yes ViennaRNA-2.5.1> * OpenMP : yes ViennaRNA-2.5.1> ViennaRNA-2.5.1> Scripting Language Interfaces ViennaRNA-2.5.1> ----------------------------- ViennaRNA-2.5.1> * Perl 5 : yes ViennaRNA-2.5.1> * Python 3.x : yes ViennaRNA-2.5.1> * Python 2.x : no ViennaRNA-2.5.1> ViennaRNA-2.5.1> Documentation ViennaRNA-2.5.1> ------------- ViennaRNA-2.5.1> * Reference Manual (PDF) : yes ViennaRNA-2.5.1> * Reference Manual (HTML) : yes ViennaRNA-2.5.1> * Tutorial (PDF) : yes ViennaRNA-2.5.1> * Tutorial (HTML) : no ViennaRNA-2.5.1> * CLA (PDF) : yes ViennaRNA-2.5.1> ViennaRNA-2.5.1> Unit Tests ViennaRNA-2.5.1> ---------- ViennaRNA-2.5.1> * Executable Programs : yes ViennaRNA-2.5.1> * C-Library : no ViennaRNA-2.5.1> * Perl 5 Interface : yes ViennaRNA-2.5.1> * Python 3.x Interface : yes ViennaRNA-2.5.1> * Python 2.x Interface : no ViennaRNA-2.5.1> ViennaRNA-2.5.1> MacOS X ViennaRNA-2.5.1> ------- ViennaRNA-2.5.1> * Universal Binary : no ViennaRNA-2.5.1> * Installer : no ViennaRNA-2.5.1> * SDK : no ViennaRNA-2.5.1> ViennaRNA-2.5.1> Install Directories ViennaRNA-2.5.1> ------------------- ViennaRNA-2.5.1> * Executables : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/bin ViennaRNA-2.5.1> * Libraries : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/lib ViennaRNA-2.5.1> * Header files : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/include ViennaRNA-2.5.1> * Extra Data : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/share ViennaRNA-2.5.1> * Man pages : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/share/man ViennaRNA-2.5.1> * Documentation : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/share/doc/ViennaRNA ViennaRNA-2.5.1> (HTML) : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/share/doc/ViennaRNA/html ViennaRNA-2.5.1> (PDF) : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/share/doc/ViennaRNA ViennaRNA-2.5.1> * Perl5 Interface : ViennaRNA-2.5.1> (binaries) : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/lib/perl5/site_perl/5.36.0/x86_64-linux-thread-multi ViennaRNA-2.5.1> (scripts) : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/lib/perl5/site_perl/5.36.0 ViennaRNA-2.5.1> * Python 3.x Interface : ViennaRNA-2.5.1> (binaries) : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/lib/python3.10/site-packages ViennaRNA-2.5.1> (scripts) : /nix/store/yx7z82c816rrqicl563k6h2zdgij4ncz-ViennaRNA-2.5.1/lib/python3.10/site-packages ViennaRNA-2.5.1> * Python 2.x Interface : Not to be installed python2 executable missing ViennaRNA-2.5.1> (binaries) : ViennaRNA-2.5.1> (scripts) : ViennaRNA-2.5.1> ViennaRNA-2.5.1> You can run 'make', 'make check', and 'make install' now! ViennaRNA-2.5.1> configurePhase completed in 2 minutes 15 seconds ViennaRNA-2.5.1> building ViennaRNA-2.5.1> build flags: SHELL=/nix/store/4xw8n979xpivdc46a9ndcvyhwgif00hz-bash-5.1-p16/bin/bash ViennaRNA-2.5.1> make all-recursive ViennaRNA-2.5.1> make[1]: Entering directory '/build/ViennaRNA-2.5.1' ViennaRNA-2.5.1> Making all in src ViennaRNA-2.5.1> make[2]: Entering directory '/build/ViennaRNA-2.5.1/src' ViennaRNA-2.5.1> Making all in ViennaRNA ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/src/ViennaRNA' ViennaRNA-2.5.1> Making all in static ViennaRNA-2.5.1> make[4]: Entering directory '/build/ViennaRNA-2.5.1/src/ViennaRNA/static' ViennaRNA-2.5.1> make all-am ViennaRNA-2.5.1> make[5]: Entering directory '/build/ViennaRNA-2.5.1/src/ViennaRNA/static' ViennaRNA-2.5.1> make[5]: Nothing to be done for 'all-am'. ViennaRNA-2.5.1> make[5]: Leaving directory '/build/ViennaRNA-2.5.1/src/ViennaRNA/static' ViennaRNA-2.5.1> make[4]: Leaving directory '/build/ViennaRNA-2.5.1/src/ViennaRNA/static' ViennaRNA-2.5.1> Making all in plotting/naview ViennaRNA-2.5.1> make[4]: Entering directory '/build/ViennaRNA-2.5.1/src/ViennaRNA/plotting/naview' ViennaRNA-2.5.1> CC naview.lo ViennaRNA-2.5.1> CCLD libRNA_naview.la ViennaRNA-2.5.1> make[4]: Leaving directory '/build/ViennaRNA-2.5.1/src/ViennaRNA/plotting/naview' ViennaRNA-2.5.1> make[4]: Entering directory '/build/ViennaRNA-2.5.1/src/ViennaRNA' ViennaRNA-2.5.1> CC fold_compound.lo ViennaRNA-2.5.1> CC dist_vars.lo ViennaRNA-2.5.1> CC part_func.lo ViennaRNA-2.5.1> CC part_func_wrappers.lo ViennaRNA-2.5.1> CC pf_fold.lo ViennaRNA-2.5.1> CC pf_multifold.lo ViennaRNA-2.5.1> CC treedist.lo ViennaRNA-2.5.1> CC inverse.lo ViennaRNA-2.5.1> CC ProfileDist.lo ViennaRNA-2.5.1> CC RNAstruct.lo ViennaRNA-2.5.1> CC mfe.lo ViennaRNA-2.5.1> CC mfe_window.lo ViennaRNA-2.5.1> CC mfe_wrappers.lo ViennaRNA-2.5.1> CC mfe_window_wrappers.lo ViennaRNA-2.5.1> CC fold.lo ViennaRNA-2.5.1> CC stringdist.lo ViennaRNA-2.5.1> CC subopt.lo ViennaRNA-2.5.1> CC subopt_zuker.lo ViennaRNA-2.5.1> CC Lfold.lo ViennaRNA-2.5.1> CC cofold.lo ViennaRNA-2.5.1> CC part_func_co.lo ViennaRNA-2.5.1> CC ProfileAln.lo ViennaRNA-2.5.1> CC duplex.lo ViennaRNA-2.5.1> CC alifold.lo ViennaRNA-2.5.1> CC alipfold.lo ViennaRNA-2.5.1> CC LPfold.lo ViennaRNA-2.5.1> CC part_func_up.lo ViennaRNA-2.5.1> CC ribo.lo ViennaRNA-2.5.1> CC MEA.lo ViennaRNA-2.5.1> CC mm.lo ViennaRNA-2.5.1> CC 2Dfold.lo ViennaRNA-2.5.1> CC 2Dpfold.lo ViennaRNA-2.5.1> CC plex_functions.lo ViennaRNA-2.5.1> CC ali_plex.lo ViennaRNA-2.5.1> CC c_plex.lo ViennaRNA-2.5.1> CC plex.lo ViennaRNA-2.5.1> CC snofold.lo ViennaRNA-2.5.1> CC snoop.lo ViennaRNA-2.5.1> CC gquad.lo ViennaRNA-2.5.1> CC perturbation_fold.lo ViennaRNA-2.5.1> CC centroid.lo ViennaRNA-2.5.1> CC model.lo ViennaRNA-2.5.1> CC dp_matrices.lo ViennaRNA-2.5.1> CC boltzmann_sampling.lo ViennaRNA-2.5.1> CC bs_wrappers.lo ViennaRNA-2.5.1> CC equilibrium_probs.lo ViennaRNA-2.5.1> CXX ../libsvm-3.25/svm.lo ViennaRNA-2.5.1> CC ../json/json.lo ViennaRNA-2.5.1> CC alphabet.lo ViennaRNA-2.5.1> CC sequence.lo ViennaRNA-2.5.1> CC unstructured_domains.lo ViennaRNA-2.5.1> CC grammar.lo ViennaRNA-2.5.1> CC heat_capacity.lo ViennaRNA-2.5.1> CC zscore.lo ViennaRNA-2.5.1> CC libRNA_concentrations_la-concentrations.lo ViennaRNA-2.5.1> CXX ../dlib-19.23/dlib/all/libRNA_concentrations_la-source.lo ViennaRNA-2.5.1> In file included from /nix/store/mmmjp0xcmr0dm307jv1l34hvi95z6d8s-glibc-2.35-224-dev/include/features.h:490, ViennaRNA-2.5.1> from /nix/store/sxdx80lmk4zkhb51f4x5dgqvxgmx55wl-gcc-11.3.0/include/c++/11.3.0/x86_64-unknown-linux-gnu/bits/os_defines.h:39, ViennaRNA-2.5.1> from /nix/store/sxdx80lmk4zkhb51f4x5dgqvxgmx55wl-gcc-11.3.0/include/c++/11.3.0/x86_64-unknown-linux-gnu/bits/c++config.h:586, ViennaRNA-2.5.1> from /nix/store/sxdx80lmk4zkhb51f4x5dgqvxgmx55wl-gcc-11.3.0/include/c++/11.3.0/string:38, ViennaRNA-2.5.1> from ../dlib-19.23/dlib/all/../base64/../algs.h:97, ViennaRNA-2.5.1> from ../dlib-19.23/dlib/all/../base64/base64_kernel_1.h:6, ViennaRNA-2.5.1> from ../dlib-19.23/dlib/all/../base64/base64_kernel_1.cpp:6, ViennaRNA-2.5.1> from ../dlib-19.23/dlib/all/source.cpp:11: ViennaRNA-2.5.1> In function 'mbstowcs', ViennaRNA-2.5.1> inlined from 'dlib::convert_mbstring_to_wstring(std::__cxx11::basic_string, std::allocator > const&)' at ../dlib-19.23/dlib/all/../unicode/unicode.cpp:155:22: ViennaRNA-2.5.1> /nix/store/mmmjp0xcmr0dm307jv1l34hvi95z6d8s-glibc-2.35-224-dev/include/bits/stdlib.h:123:12: warning: '*mbstowcs' specified size 18446744073709551600 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] ViennaRNA-2.5.1> 123 | return __glibc_fortify_n (mbstowcs, __len, sizeof (wchar_t), ViennaRNA-2.5.1> | ^~~~~~~~~~~~~~~~~ ViennaRNA-2.5.1> /nix/store/mmmjp0xcmr0dm307jv1l34hvi95z6d8s-glibc-2.35-224-dev/include/bits/stdlib.h: In function 'dlib::convert_mbstring_to_wstring(std::__cxx11::basic_string, std::allocator > const&)': ViennaRNA-2.5.1> /nix/store/mmmjp0xcmr0dm307jv1l34hvi95z6d8s-glibc-2.35-224-dev/include/bits/stdlib.h:104:15: note: in a call to function '*mbstowcs' declared with attribute 'access (write_only, 1, 3)' ViennaRNA-2.5.1> 104 | extern size_t __REDIRECT_NTH (__mbstowcs_alias, ViennaRNA-2.5.1> | ^~~~~~~~~~~~~~ ViennaRNA-2.5.1> CXX libRNA_concentrations_la-wrap_dlib.lo ViennaRNA-2.5.1> CXXLD libRNA_concentrations.la ViennaRNA-2.5.1> CC constraints/constraints.lo ViennaRNA-2.5.1> CC constraints/SHAPE.lo ViennaRNA-2.5.1> CC constraints/hard.lo ViennaRNA-2.5.1> CC constraints/soft.lo ViennaRNA-2.5.1> CC constraints/ligand.lo ViennaRNA-2.5.1> CCLD libRNA_constraints.la ViennaRNA-2.5.1> CC datastructures/basic_datastructures.lo ViennaRNA-2.5.1> CC datastructures/lists.lo ViennaRNA-2.5.1> CC datastructures/char_stream.lo ViennaRNA-2.5.1> CC datastructures/stream_output.lo ViennaRNA-2.5.1> CC datastructures/hash_tables.lo ViennaRNA-2.5.1> CC datastructures/heap.lo ViennaRNA-2.5.1> CCLD libRNA_datastructures.la ViennaRNA-2.5.1> CC utils/utils.lo ViennaRNA-2.5.1> CC utils/string_utils.lo ViennaRNA-2.5.1> CC utils/structure_utils.lo ViennaRNA-2.5.1> CC utils/structure_tree.lo ViennaRNA-2.5.1> CC utils/msa_utils.lo ViennaRNA-2.5.1> CC utils/higher_order_functions.lo ViennaRNA-2.5.1> CC utils/cpu.lo ViennaRNA-2.5.1> CC utils/units.lo ViennaRNA-2.5.1> CC io/io_utils.lo ViennaRNA-2.5.1> CC io/file_formats.lo ViennaRNA-2.5.1> CC io/file_formats_msa.lo ViennaRNA-2.5.1> CC search/BoyerMoore.lo ViennaRNA-2.5.1> CC commands.lo ViennaRNA-2.5.1> CC combinatorics.lo ViennaRNA-2.5.1> CC utils/svm_utils.lo ViennaRNA-2.5.1> CCLD libRNA_utils.la ViennaRNA-2.5.1> CC plotting/alignments.lo ViennaRNA-2.5.1> CC plotting/layouts.lo ViennaRNA-2.5.1> CC plotting/probabilities.lo ViennaRNA-2.5.1> CC plotting/structures.lo ViennaRNA-2.5.1> CC plotting/plot_utils.lo ViennaRNA-2.5.1> CC plotting/RNApuzzler/RNApuzzler.lo ViennaRNA-2.5.1> CC plotting/RNApuzzler/RNAturtle.lo ViennaRNA-2.5.1> CCLD libRNA_plotting.la ViennaRNA-2.5.1> CC params/io.lo ViennaRNA-2.5.1> CC params/default.lo ViennaRNA-2.5.1> CC params/params.lo ViennaRNA-2.5.1> CC params/convert.lo ViennaRNA-2.5.1> CCLD libRNA_params.la ViennaRNA-2.5.1> CC eval.lo ViennaRNA-2.5.1> CC eval_covariance.lo ViennaRNA-2.5.1> CC eval_wrappers.lo ViennaRNA-2.5.1> CCLD libRNA_eval.la ViennaRNA-2.5.1> CC loops/external.lo ViennaRNA-2.5.1> CC loops/external_bt.lo ViennaRNA-2.5.1> CC loops/external_pf.lo ViennaRNA-2.5.1> CC loops/hairpin.lo ViennaRNA-2.5.1> CC loops/hairpin_bt.lo ViennaRNA-2.5.1> CC loops/hairpin_pf.lo ViennaRNA-2.5.1> CC loops/internal.lo ViennaRNA-2.5.1> CC loops/internal_bt.lo ViennaRNA-2.5.1> CC loops/internal_pf.lo ViennaRNA-2.5.1> CC loops/multibranch.lo ViennaRNA-2.5.1> CC loops/multibranch_bt.lo ViennaRNA-2.5.1> CC loops/multibranch_pf.lo ViennaRNA-2.5.1> CCLD libRNA_loops.la ViennaRNA-2.5.1> CC move_set.lo ViennaRNA-2.5.1> CC landscape/move.lo ViennaRNA-2.5.1> CC landscape/findpath.lo ViennaRNA-2.5.1> CC landscape/neighbor.lo ViennaRNA-2.5.1> CC landscape/walk.lo ViennaRNA-2.5.1> CCLD libRNA_landscape.la ViennaRNA-2.5.1> CC utils/libRNA_utils_sse41_la-higher_order_functions_sse41.lo ViennaRNA-2.5.1> CCLD libRNA_utils_sse41.la ViennaRNA-2.5.1> CC utils/libRNA_utils_avx512_la-higher_order_functions_avx512.lo ViennaRNA-2.5.1> CCLD libRNA_utils_avx512.la ViennaRNA-2.5.1> CXXLD libRNA_conv.la ViennaRNA-2.5.1> CXXLD libRNA.la ViennaRNA-2.5.1> CC special_const.lo ViennaRNA-2.5.1> CC ugly_bt.lo ViennaRNA-2.5.1> CCLD libRNA_special_const.la ViennaRNA-2.5.1> GEN libRNA.a ViennaRNA-2.5.1> make[4]: Leaving directory '/build/ViennaRNA-2.5.1/src/ViennaRNA' ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/src/ViennaRNA' ViennaRNA-2.5.1> Making all in bin ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/src/bin' ViennaRNA-2.5.1> CC RNAfold_cmdl.o ViennaRNA-2.5.1> CC RNAfold.o ViennaRNA-2.5.1> CC input_id_helpers.lo ViennaRNA-2.5.1> CC parallel_helpers.lo ViennaRNA-2.5.1> CC ../cthreadpool/thpool.lo ViennaRNA-2.5.1> CCLD libhelpers.la ViennaRNA-2.5.1> CCLD RNAfold ViennaRNA-2.5.1> CC RNAeval_cmdl.o ViennaRNA-2.5.1> CC RNAeval.o ViennaRNA-2.5.1> CCLD RNAeval ViennaRNA-2.5.1> CC RNAheat_cmdl.o ViennaRNA-2.5.1> CC RNAheat.o ViennaRNA-2.5.1> CCLD RNAheat ViennaRNA-2.5.1> CC RNApdist_cmdl.o ViennaRNA-2.5.1> CC RNApdist.o ViennaRNA-2.5.1> CCLD RNApdist ViennaRNA-2.5.1> CC RNAdistance_cmdl.o ViennaRNA-2.5.1> CC RNAdistance.o ViennaRNA-2.5.1> CCLD RNAdistance ViennaRNA-2.5.1> CC RNAinverse_cmdl.o ViennaRNA-2.5.1> CC RNAinverse.o ViennaRNA-2.5.1> CCLD RNAinverse ViennaRNA-2.5.1> CC RNAplot_cmdl.o ViennaRNA-2.5.1> CC RNAplot.o ViennaRNA-2.5.1> CCLD RNAplot ViennaRNA-2.5.1> CC RNAsubopt_cmdl.o ViennaRNA-2.5.1> CC RNAsubopt.o ViennaRNA-2.5.1> CCLD RNAsubopt ViennaRNA-2.5.1> CC RNALfold_cmdl.o ViennaRNA-2.5.1> CC RNALfold.o ViennaRNA-2.5.1> CCLD RNALfold ViennaRNA-2.5.1> CC RNAcofold_cmdl.o ViennaRNA-2.5.1> CC RNAcofold.o ViennaRNA-2.5.1> CCLD RNAcofold ViennaRNA-2.5.1> CC RNApaln_cmdl.o ViennaRNA-2.5.1> CC RNApaln.o ViennaRNA-2.5.1> CCLD RNApaln ViennaRNA-2.5.1> CC RNAduplex_cmdl.o ViennaRNA-2.5.1> CC RNAduplex.o ViennaRNA-2.5.1> CCLD RNAduplex ViennaRNA-2.5.1> CC RNAalifold_cmdl.o ViennaRNA-2.5.1> CC RNAalifold.o ViennaRNA-2.5.1> CCLD RNAalifold ViennaRNA-2.5.1> CC RNAplfold_cmdl.o ViennaRNA-2.5.1> CC RNAplfold.o ViennaRNA-2.5.1> CCLD RNAplfold ViennaRNA-2.5.1> CC RNAup_cmdl.o ViennaRNA-2.5.1> CC RNAup.o ViennaRNA-2.5.1> CCLD RNAup ViennaRNA-2.5.1> CC RNAaliduplex_cmdl.o ViennaRNA-2.5.1> CC RNAaliduplex.o ViennaRNA-2.5.1> CCLD RNAaliduplex ViennaRNA-2.5.1> CC RNALalifold_cmdl.o ViennaRNA-2.5.1> CC RNALalifold.o ViennaRNA-2.5.1> CCLD RNALalifold ViennaRNA-2.5.1> CC RNA2Dfold_cmdl.o ViennaRNA-2.5.1> CC RNA2Dfold.o ViennaRNA-2.5.1> CCLD RNA2Dfold ViennaRNA-2.5.1> CC RNAparconv_cmdl.o ViennaRNA-2.5.1> CC RNAparconv.o ViennaRNA-2.5.1> CCLD RNAparconv ViennaRNA-2.5.1> CC RNAPKplex_cmdl.o ViennaRNA-2.5.1> CC RNAPKplex.o ViennaRNA-2.5.1> CCLD RNAPKplex ViennaRNA-2.5.1> CC RNAplex_cmdl.o ViennaRNA-2.5.1> CC RNAplex.o ViennaRNA-2.5.1> CCLD RNAplex ViennaRNA-2.5.1> CC RNAsnoop_cmdl.o ViennaRNA-2.5.1> CC RNAsnoop.o ViennaRNA-2.5.1> CCLD RNAsnoop ViennaRNA-2.5.1> CC RNApvmin_cmdl.o ViennaRNA-2.5.1> CC RNApvmin.o ViennaRNA-2.5.1> CCLD RNApvmin ViennaRNA-2.5.1> CC RNAdos_cmdl.o ViennaRNA-2.5.1> CC RNAdos.o ViennaRNA-2.5.1> CCLD RNAdos ViennaRNA-2.5.1> CC RNAmultifold_cmdl.o ViennaRNA-2.5.1> CC RNAmultifold.o ViennaRNA-2.5.1> CCLD RNAmultifold ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/src/bin' ViennaRNA-2.5.1> Making all in Utils ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/src/Utils' ViennaRNA-2.5.1> CC b2ct.o ViennaRNA-2.5.1> CCLD b2ct ViennaRNA-2.5.1> CC popt.o ViennaRNA-2.5.1> CCLD popt ViennaRNA-2.5.1> CC ct2db_cmdl.o ViennaRNA-2.5.1> CC ct2db.o ViennaRNA-2.5.1> CCLD ct2db ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/src/Utils' ViennaRNA-2.5.1> Making all in Cluster ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/src/Cluster' ViennaRNA-2.5.1> CC split.o ViennaRNA-2.5.1> CC distance_matrix.o ViennaRNA-2.5.1> CC cluster.o ViennaRNA-2.5.1> CC treeplot.o ViennaRNA-2.5.1> CC AD_main.o ViennaRNA-2.5.1> CCLD AnalyseDists ViennaRNA-2.5.1> CC statgeom.o ViennaRNA-2.5.1> CC AS_main.o ViennaRNA-2.5.1> CC PS3D.o ViennaRNA-2.5.1> CCLD AnalyseSeqs ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/src/Cluster' ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/src' ViennaRNA-2.5.1> make[3]: Nothing to be done for 'all-am'. ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/src' ViennaRNA-2.5.1> make[2]: Leaving directory '/build/ViennaRNA-2.5.1/src' ViennaRNA-2.5.1> Making all in man ViennaRNA-2.5.1> make[2]: Entering directory '/build/ViennaRNA-2.5.1/man' ViennaRNA-2.5.1> make[2]: Nothing to be done for 'all'. ViennaRNA-2.5.1> make[2]: Leaving directory '/build/ViennaRNA-2.5.1/man' ViennaRNA-2.5.1> Making all in misc ViennaRNA-2.5.1> make[2]: Entering directory '/build/ViennaRNA-2.5.1/misc' ViennaRNA-2.5.1> make[2]: Nothing to be done for 'all'. ViennaRNA-2.5.1> make[2]: Leaving directory '/build/ViennaRNA-2.5.1/misc' ViennaRNA-2.5.1> Making all in doc ViennaRNA-2.5.1> make[2]: Entering directory '/build/ViennaRNA-2.5.1/doc' ViennaRNA-2.5.1> Making all in CLA ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/doc/CLA' ViennaRNA-2.5.1> make[3]: Nothing to be done for 'all'. ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/doc/CLA' ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/doc' ViennaRNA-2.5.1> make[3]: Nothing to be done for 'all-am'. ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/doc' ViennaRNA-2.5.1> make[2]: Leaving directory '/build/ViennaRNA-2.5.1/doc' ViennaRNA-2.5.1> Making all in RNA-Tutorial ViennaRNA-2.5.1> make[2]: Entering directory '/build/ViennaRNA-2.5.1/RNA-Tutorial' ViennaRNA-2.5.1> make[2]: Nothing to be done for 'all'. ViennaRNA-2.5.1> make[2]: Leaving directory '/build/ViennaRNA-2.5.1/RNA-Tutorial' ViennaRNA-2.5.1> Making all in interfaces ViennaRNA-2.5.1> make[2]: Entering directory '/build/ViennaRNA-2.5.1/interfaces' ViennaRNA-2.5.1> Making all in Perl ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/interfaces/Perl' ViennaRNA-2.5.1> CXX RNA_la-RNA_wrap.lo ViennaRNA-2.5.1> CXXLD RNA.la ViennaRNA-2.5.1> In function 'mbstowcs', ViennaRNA-2.5.1> inlined from 'convert_mbstring_to_wstring' at ../../src/ViennaRNA/../dlib-19.23/dlib/all/../unicode/unicode.cpp:155:22: ViennaRNA-2.5.1> /nix/store/mmmjp0xcmr0dm307jv1l34hvi95z6d8s-glibc-2.35-224-dev/include/bits/stdlib.h:123:12: warning: '__mbstowcs_alias' specified size 18446744073709551600 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] ViennaRNA-2.5.1> 123 | return __glibc_fortify_n (mbstowcs, __len, sizeof (wchar_t), ViennaRNA-2.5.1> | ^ ViennaRNA-2.5.1> /nix/store/mmmjp0xcmr0dm307jv1l34hvi95z6d8s-glibc-2.35-224-dev/include/bits/stdlib.h: In function 'convert_mbstring_to_wstring': ViennaRNA-2.5.1> /nix/store/mmmjp0xcmr0dm307jv1l34hvi95z6d8s-glibc-2.35-224-dev/include/bits/stdlib.h:104:15: note: in a call to function '__mbstowcs_alias' declared with attribute 'access (write_only, 1, 3)' ViennaRNA-2.5.1> 104 | extern size_t __REDIRECT_NTH (__mbstowcs_alias, ViennaRNA-2.5.1> | ^ ViennaRNA-2.5.1> GEN auto/RNA/RNA.so ViennaRNA-2.5.1> make[3]: Leaving directory '/build/ViennaRNA-2.5.1/interfaces/Perl' ViennaRNA-2.5.1> Making all in Python ViennaRNA-2.5.1> make[3]: Entering directory '/build/ViennaRNA-2.5.1/interfaces/Python' ViennaRNA-2.5.1> CXX _RNA_la-RNA_wrap.lo ViennaRNA-2.5.1> CXXLD _RNA.la error: timed out after 1200 seconds