[v2.6.4.b] Possible long-option typo for --ntree in src/R-scape.c and TORNADO parser build workaround

[Jiren-Zhou]

Hi R-scape team,

These notes are based on my build experience with R-scape (v2.6.4.b).

1. Possible long-option typo around --ntree

File: 'src/R-scape.c'
Location: around line ~788 (v2.6.4.b)

I noticed the long option for the tree number appears to use a single dash:

Current in code: '-ntree'

Expected: '--ntree'

2. TORNADO build may require manual parser generation + low parallelism

2.1 Manually generate the parser files under 'lib/tornado/src'

'''
cd ~/phyloRNA/tools/rscape_v2.6.4.b

make

cd ~/phyloRNA/tools/rscape_v2.6.4.b/lib/tornado/src

make clean
bison -d -o grm_parsegrammar.tab.c grm_parsegrammar.y

ls -l grm_parsegrammar.tab.h grm_parsegrammar.tab.c

make -j1

cd ~/phyloRNA/tools/rscape_v2.6.4.b
make clean
make -j
'''

Thanks!

[RivasLab]

thanks for your input. 1. has been taken care of. 2. can you explain more the issue you encountered building tornado automatically? thank you Elena

…

On Dec 9, 2025, at 19:38, Jiren-Zhou ***@***.***> wrote: Jiren-Zhou created an issue (EddyRivasLab/R-scape#8) Hi R-scape team, These notes are based on my build experience with R-scape (v2.6.4.b). 1. Possible long-option typo around --ntree File: 'src/R-scape.c' Location: around line ~788 (v2.6.4.b) I noticed the long option for the tree number appears to use a single dash: Current in code: '-ntree' Expected: '--ntree' 2. TORNADO build may require manual parser generation + low parallelism 2.1 Manually generate the parser files under 'lib/tornado/src' ''' cd ~/phyloRNA/tools/rscape_v2.6.4.b make cd ~/phyloRNA/tools/rscape_v2.6.4.b/lib/tornado/src make clean bison -d -o grm_parsegrammar.tab.c grm_parsegrammar.y ls -l grm_parsegrammar.tab.h grm_parsegrammar.tab.c make -j1 cd ~/phyloRNA/tools/rscape_v2.6.4.b make clean make -j ''' Thanks! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Jiren-Zhou]

The issue I encountered is that when compiling R-scape 2.6.4.b, the build fails inside lib/tornado/src with repeated errors like:

'fatal error: grm_parsegrammar.tab.h: No such file or directory.'

I analyzed and resolved this problem. In my case, this error only occurs when Bison is missing in the current environment, because the Bison-generated parser files are not created before compilation begins.

My solution is to manually generate the parser files with Bison in:

'lib/tornado/src'

then return to the tornado directory and compile with low concurrency, and finally go back to the main R-scape directory to complete the build. The compilation can then pass successfully.

Additionally,
The failure happens because 'grm_parsegrammar.tab.h/.c' are not guaranteed to be generated before compiling dependent sources.

Add a Makefile rule to generate both files from 'grm_parsegrammar.y', and make all 'grm-*.o' that include the header depend on 'grm_parsegrammar.tab.h'

Add a friendly error if 'bison' is missing.

[AntonPetrov]

I confirm that R-scape won’t build without bison, and in addition I have to use the following steps to install it in a modern Debian-based Docker image because R-scape and several of its bundled subprojects ship very old autotools machinery (including outdated config.guess / config.sub and stale configure/Makefile.in files). These legacy build scripts fail on current Linux distributions—especially on newer architectures—so the build requires:

• Installing bison (or the build stops early)
• Updating config.guess / config.sub so modern CPU/OS triplets are recognised
• Regenerating autotools in R2R and Tornado
• Forcing explicit --build / --host triplets to avoid mis-detection by old config scripts

Without these compatibility steps, the build consistently errors out.

Here is the block I use in my Dockerfile:

RUN set -eux; \
    wget --no-verbose -O - "http://rivaslab.org/software/rscape/rscape_${RSCAPE_VER}.tar.gz" | tar zxf -; \
    mv "rscape_${RSCAPE_VER}" rscape; \
    # pick newest available config.guess/config.sub (prefer autotools-dev location)
    CONFIG_DIR="/usr/share/misc"; \
    if [ ! -f "$CONFIG_DIR/config.guess" ] || [ ! -f "$CONFIG_DIR/config.sub" ]; then \
      CONFIG_DIR="/usr/share/automake-1.16"; \
    fi; \
    # refresh config.guess/config.sub for subprojects that ship very old versions
    if [ -f "$CONFIG_DIR/config.guess" ] && [ -f "$CONFIG_DIR/config.sub" ]; then \
      for subdir in \
        /tmp/build/rscape/lib/R2R/R2R-current \
        /tmp/build/rscape/lib/tornado \
        /tmp/build/rscape/lib/infernal \
        /tmp/build/rscape/lib/hmmer \
        /tmp/build/rscape \
      ; do \
        if [ -d "$subdir" ]; then \
          cp "$CONFIG_DIR/config.guess" "$subdir"/config.guess || true; \
          cp "$CONFIG_DIR/config.sub"   "$subdir"/config.sub   || true; \
        fi; \
      done; \
    fi; \
    # Regenerate build systems where needed (R2R and Tornado)
    cd rscape/lib/R2R/R2R-current && autoreconf -f && cd /tmp/build/rscape; \
    if [ -d rscape/lib/tornado ]; then \
      cd rscape/lib/tornado && autoreconf -f || true; \
      cd /tmp/build/rscape; \
    fi; \
    if [ -d rscape/lib/infernal ]; then \
      cd rscape/lib/infernal && autoreconf -f || true; \
      cd /tmp/build/rscape; \
    fi; \
    # Force build/host triplets to avoid ancient config.guess failures in subprojects
    BUILD_TRIPLET="$(gcc -dumpmachine)"; \
    ./configure --prefix=/opt/rscape --build="$BUILD_TRIPLET" --host="$BUILD_TRIPLET"; \
    make -j1; \
    make install

[RivasLab]

Hello, thanks to both of you for the input. I have created a new version of R-scape v2.6.4.c (downloadable from rivaslab.org).

• In this version, all config.guess and config.sub files have been updated to automake 1.18.
• At installation, it checks for "bison" and if it is not present, it continues w/o installing tornado. Tornado is not use directly by R-scape or any R-scape flags at the moment. I haven't been able to test that this work as expected. Happy to take input back.
• I don't have a solution for having to do autoreconf -f with R2R. The issue persist for now.
• The typo on the --ntree option is fixed.

Thanks for your comments and input.

[AntonPetrov]

Hi Elena,

I tried building v2.6.4.c in a clean Docker environment (using the official python:3.13-slim image as a base), and even with bison (and flex) not installed, configure succeeds but make still descends into lib/tornado and fails with:

SUBDIR @TORNADO_ESLDIR@
make[2]: *** @TORNADO_ESLDIR@: No such file or directory.  Stop.

This suggests that Tornado is still being pulled into the build.

At the same time, configure appears to require lib/tornado/Makefile.in to exist (so Tornado is expected at configure time even if it’s meant to be skipped later).

Happy to test a fix if it helps. Thank you!

[RivasLab]

Many thanks for your patience and invaluable support. R-scape v2.6.4.d is available at rivaslab.org.
It checks for bison, and ignores tornado altogether if not found.

Hope this works, please let me know otherwise, and sorry for the many tries on this!