Stop with error during make step of the IntaRNA installation

[MicSonn]

Dear IntaRNA developers,
I'm trying to install IntaRNA. During make step obtaining this sentence:

make[3]: Entering directory '/media/standard/SSD1/data/tools/intaRNA-3.4.1/src/IntaRNA'
CXX Accessibility.o
CXX AccessibilityConstraint.o
CXX AccessibilityFromStream.o
CXX AccessibilityVrna.o
AccessibilityVrna.cpp: In static member function ‘static void IntaRNA::AccessibilityVrna::addConstraints(vrna_fold_compound_t&, const IntaRNA::Accessibility&)’:
AccessibilityVrna.cpp:164:4: error: ‘vrna_constraints_add_SHAPE’ was not declared in this scope; did you mean ‘vrna_constraints_add’?
164 | vrna_constraints_add_SHAPE(&fold_compound,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
| vrna_constraints_add
make[3]: *** [Makefile:766: AccessibilityVrna.o] Error 1
make[3]: Leaving directory '/media/standard/SSD1/data/tools/intaRNA-3.4.1/src/IntaRNA'
make[2]: *** [Makefile:578: all-recursive] Error 1
make[2]: Leaving directory '/media/standard/SSD1/data/tools/intaRNA-3.4.1/src'
make[1]: *** [Makefile:437: all] Error 2
make[1]: Leaving directory '/media/standard/SSD1/data/tools/intaRNA-3.4.1/src'
make: *** [Makefile:424: all-recursive] Error 1

My distro:
Distributor ID: Ubuntu
Description: Ubuntu 20.04.6 LTS
Release: 20.04
Codename: focal

installed version Vienna library: ViennaRNA-2.7.1

Commands provided after Vienna installation:

1. ./configure --with-vrna=/media/standard/SSD1/data/tools/ViennaRNA
2. make

Please, how can I solve this?

Best,
MicSonn!

START ======================================================
output of ./configure --with-vrna=/media/standard/SSD1/data/tools/ViennaRNA

checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether ln -s works... yes
checking for ranlib... ranlib
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports the include directive... yes (GNU style)
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking dependency style of g++... gcc3
checking whether g++ supports C++11 features by default... yes
checking for a Python interpreter with version >= 3.6... python
checking for python... /home/standard/anaconda3/bin/python
checking for python version... 3.8
checking for python platform... linux
checking for python script directory... ${prefix}/lib/python3.8/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python3.8/site-packages
checking for pkg-config... /home/linuxbrew/.linuxbrew/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking whether make supports nested variables... (cached) yes
checking whether to use and provide pkg-config information... yes
checking for pkg-config... yes
checking whether to build with debug information... no
checking whether to build statically linked binaries... no
checking whether to enable multi-threading support... yes
checking for OpenMP flag of C++ compiler... -fopenmp
checking whether to use a multi-precision partition function data type (quadmath)... no
checking for doxygen... no
checking whether to enable coloring of console log output... yes
checking whether to compile and install 'intarnapvalue' python module... no
checking for boostlib >= 1.50.0 (105000)... yes
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system... yes
checking whether the Boost::Filesystem library is available... yes
checking for exit in -lboost_filesystem... yes
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for size_t... yes
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
configure: check if VRNA version >= 2.4.14
checking for VRNA... yes
checking for compilation with Vienna RNA package headers... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/IntaRNA/Makefile
config.status: creating src/IntaRNA/intarna_config.h
config.status: creating src/bin/Makefile
config.status: creating perl/Makefile
config.status: creating R/Makefile
config.status: creating python/Makefile
config.status: creating python/bin/Makefile
config.status: creating python/intarnapvalue/Makefile
config.status: creating python/copomus/Makefile
config.status: creating tests/Makefile
config.status: creating tests/data/Makefile
config.status: creating doc/Makefile
config.status: creating IntaRNA.pc
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands
configure:

======================================
IntaRNA 3.4.1

Features

• log coloring : yes
• OpenMP multi-threading : yes
• intarnapvalue : no

Install Directories for given 'prefix'

• Install prefix : /usr/local
• Executables : /usr/local/bin
• Libraries : /usr/local/lib
• Header files : /usr/local/include
• Python modules :

You can run 'make', 'make tests' and 'make install' now!

Run 'make install prefix=XYZ' for installation in an alternative directory.

================================================================ END

[martin-raden]

Hi @MicSonn

thanks for the notification.
I checked and found that the recent RNA vienna package update to 2.7.1 caused a change in the API and (re)moved the function we are using to a different location.. 🤔

Please downgrade your viennarna version to 2.7.0 and it should work fine.

I will contact the viennarna people if they are aware of the API break and what to do about it..

Best,
Martin

[MicSonn]

Hi Martin,
everything's fine with version 2.7.0
Thanks.

Best,
Michele