Instalation failed on Fedora 36

[NatashaJorge]

Hi,

I've been trying to install sybilSBML without any success.

I've installed libSBML without any problems with:

$ R CMD INSTALL libSBML_5.19.0.tar.gz

I'm inside a conda environment, so the path for library and include are different. I give them to sybilSBML during installation with:

$ R CMD INSTALL --configure-args="--with-sbml-include=/homes/brauerei/natasha/miniconda3/envs/bacarena/include/ --with-sbml-lib=/homes/brauerei/natasha/miniconda3/envs/bacarena/lib/" sybilSBML_3.1.3.tar.gz

However there are always the same error:

checking sbml/SBMLTypes.h usability... yes
checking sbml/SBMLTypes.h presence... sed: can't read conftest.c: No such file or directory
no
configure: WARNING: sbml/SBMLTypes.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: sbml/SBMLTypes.h: proceeding with the compiler's result
checking for sbml/SBMLTypes.h... yes
checking for library containing readSBML... no
configure: error: Could not link to libSBML:
use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.
ERROR: configuration failed for package ‘sybilSBML’

• removing ‘/homes/brauerei/natasha/miniconda3/envs/bacarena/lib/R/library/sybilSBML’

Please, how could I install sybilSBML?

best wishes,
Natasha

[mixiaoluo88]

hi,

Thank you so much for your exceptional software.

However, I encountered the similar problem, all of the attempts of which lead to the message "checking for library containing readSBML... no".

here are my command steps:

wget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/Linux/64-bit/libSBML-5.18.0-Linux-x64.deb
wget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/R%20interface/libSBML_5.18.0.tar.gz
sudo apt install ./libSBML-5.18.0-Linux-x64.deb 
R CMD INSTALL libSBML_5.18.0.tar.gz
install.packages("remotes")
remotes::install_github("SysBioChalmers/sybil-SBML")

the error log is as follows:

> remotes::install_github("SysBioChalmers/sybil-SBML",configure.args="--with-sbml-lib=/usr/local/lib --with-sbml-include=/usr/local/include --with-sbml-libs='-lsbml'")
Downloading GitHub repo SysBioChalmers/sybil-SBML@HEAD
Skipping 1 packages not available: sybil
Running `R CMD build`...
* checking for file ‘/tmp/RtmpBaHB0f/remotesba8f8681e7f59/SysBioChalmers-sybil-SBML-8756890/DESCRIPTION’ ... OK
* preparing ‘sybilSBML’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘sybilSBML_3.1.3.tar.gz’
/mnt/raid1/lvhy/miniconda3/envs/COBRA/lib/R/bin/exec/R: /mnt/raid1/lvhy/miniconda3/envs/COBRA/lib/R/bin/exec/../../lib/../.././libtinfo.so.6: no version information available (required by /mnt/raid1/lvhy/miniconda3/envs/COBRA/lib/R/bin/exec/../../lib/../../libreadline.so.8)
* installing *source* package ‘sybilSBML’ ...
** using staged installation
configure: WARNING: unrecognized options: --with-sbml-libs
checking for gcc... x86_64-conda-linux-gnu-cc
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 x86_64-conda-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-conda-linux-gnu-cc -E
checking for pkg-config... /usr/bin/pkg-config
configure: set compile and link flags according to pkg-config
configure: compile flags are -I/usr/local/include -I/usr/include/libxml2
configure: link flags are -L/usr/local/lib -lsbml
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... no
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 sbml/SBMLTypes.h usability... yes
checking sbml/SBMLTypes.h presence... yes
checking for sbml/SBMLTypes.h... yes
checking for library containing readSBML... no
configure: error: Could not link to libSBML:
      use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.
ERROR: configuration failed for package ‘sybilSBML’
* removing ‘/mnt/raid1/lvhy/miniconda3/envs/COBRA/lib/R/library/sybilSBML’
Warning message:
In i.p(...) :

and i also tried the script from https://gist.github.com/dosorio/ea4baf66ee68821014d7dc6d92a48c55, it doesn't work for me.

Thank you again for your efforts and look forward to your reply as soon as possible!

hongyang lvy.

[mihai-sysbio]

@mixiaoluo88 thanks for reaching out.

Have you tried following the latest installation instructions? Here is the part that I'm thinking might help in your case:

"If the above fails because of failing to load libsbml.so, try adding the path to this file before starting R:"

LD_LIBRARY_PATH=/usr/lib64 R

[mixiaoluo88]

@mihai-sysbio Thank you for your response. I have attempted to follow the latest installation guide, but it appears that the issue may be related to my environment or another factor. Despite passing the option --with-sbml-include=/usr/local/include/ --with-sbml-lib=/usr/local/lib/ when installing sybil-SBML, R was unable to locate the file libsbml.so.

However, I have now successfully installed and run the software by creating a Singularity container.

Thank you once again for your assistance!

[mihai-sysbio]

Great to hear you got it to run!

the issue may be related to my environment or another factor

If you'd like to, it could be included in the documentation.

creating a Singularity container

If you'd be willing to share that, I'm happy to include it in the repository.

[mixiaoluo88]

@mihai-sysbio Hello, I have installed the sybil-SBML software primarily to convert the RDS files generated by gapseq into SBML format data. However, I am unsure if the packaged singularity container will be beneficial for directly using the sybil-SBML software.
Below is the recipe file named singularity.build_gapseq that I utilized to build the container:

Bootstrap: docker
From: ubuntu:20.04

%post
    # install gapseq
    apt-get update
    DEBIAN_FRONTEND=noninteractive apt-get install -y ncbi-blast+ git libglpk-dev r-base-core exonerate bedtools barrnap bc parallel libcurl4-openssl-dev libssl-dev locales locales-all wget curl
    R -e 'install.packages(c("data.table", "stringr", "sybil", "getopt", "doParallel", "foreach", "R.utils", "stringi", "glpkAPI", "CHNOSZ", "jsonlite", "httr"))'
    R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
    cd /usr/local && git clone https://github.com/jotech/gapseq && cd gapseq && ln -s $PWD/gapseq /usr/local/bin/
    gapseq test
    cd /usr/local/gapseq && bash /usr/local/gapseq/src/update_sequences.sh
    # install sybil and sybil-SBML
    cd /usr/local/ && \
    wget https://cran.r-project.org/src/contrib/Archive/sybil/sybil_2.2.0.tar.gz && \
    R CMD INSTALL sybil_2.2.0.tar.gz
    apt install libxml2-dev
    mkdir -p /usr/local/sybilSBML
    cd /usr/local/sybilSBML
    wget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/Linux/64-bit/libSBML-5.18.0-Linux-x64.deb
    apt install ./libSBML-5.18.0-Linux-x64.deb  
    wget https://downloads.sourceforge.net/project/sbml/libsbml/5.17.0/stable/libSBML-5.17.0-core-plus-packages-src.tar.gz
    tar -xxvf libSBML-5.17.0-core-plus-packages-src.*
    cd libSBML-5.17.0-Source
    ./configure --prefix=/usr/local/ \
            --enable-cpp-namespace \
            --enable-fbc \
            --enable-shared \
            --with-gnu-ld \
            --enable-layout \
            --enable-comp \
            --enable-qual \
            --enable-groups \
            --enable-compression \
            --enable-shared-version
    make
    make install
    cd ..
    ldconfig
    export DYLD_LIBRARY_PATH=/usr/local/lib
    wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.0.1.tar.gz
    ls /usr/local/lib
    R CMD INSTALL sybilSBML_3.0.1.tar.gz

To build, use the command: :singularity build --fakeroot gapseq_image.sif singularity.build_gapseq

Please note that gapseq generates temporary files under the path /install/path/to/gapseq/dat during operation. Therefore, in addition to mounting the input file path into the container, you also need to mount the gapseq/dat path. The command to run gapseq is as follows: singularity exec -B /absolute/path/to/inputdat:/mnt/inputdata -B /local/env/install/path/to/gapseq/dat:/usr/local/gapseq/dat /loacl/image_pipeline/gapseq_image.sif /usr/local/gapseq/gapseq doall /mnt/inputdata/test_strain.fna

I hope this information is helpful to you!