Installation error linux: template with C linkage

[hexylena]

Hi developers, apologies if I've missed any discussion of this in my searches but I'm struggling to install it cleanly from the conda environment.

I'm installing it in a container just for maximum reproducibility for myself. I'm building it from the 1.0.0 tag of this git repository.

Dockerfile (Conda)

This is based on the way seqera wave does its docker containers for conda packages, if you have suggestions for changing it I'm very open to it!!

FROM mambaorg/micromamba:2.3.0-debian11

WORKDIR /methylasso

USER root
RUN apt -y update && apt install -y git
RUN git clone -b v1.0.0 https://github.com/bardetlab/methylasso .

RUN micromamba install -y -n base -f conda_env.yml \
    && micromamba install -y -n base gcc gxx conda-forge::procps-ng \
    && micromamba env export --name base --explicit > environment.lock \
    && echo ">> CONDA_LOCK_START" \
    && cat environment.lock \
    && echo "<< CONDA_LOCK_END" \
    && micromamba clean -a -y
# USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"

RUN R CMD INSTALL --preclean .

ENTRYPOINT ["Rscript", "/methylasso/MethyLasso.R"]

The conda version fails to build completely for me, when it gets to the compilation stage, that's when I encounter the following:

(base) root@0774d45c02b7:/methylasso# R CMD INSTALL .                                                    
* installing to library ‘/opt/conda/lib/R/library’                                                      
* installing *source* package ‘MethyLasso’ ...
** using staged installation                                                                            
** libs                                                                                                 
using C++ compiler: ‘x86_64-conda-linux-gnu-c++ (conda-forge gcc 15.1.0-3) 15.1.0’
using C++11                                                                                             
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I"core" -I"core/gfl" -I'/opt/conda/lib/R/library/Rcpp/include' -I'/opt/conda/lib/R/library/RcppEigen/include' -I'/opt/conda/lib/R
/library/BH/include' -I'/opt/conda/lib/R/library/RcppGSL/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib    -fpic  -fvisibility-inline
s-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feed
stock_root/build_artifacts/r-base-split_1747311161993/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix  -c core/GFLLibrary1DAdamtsImpl.cpp -o core/GFLLibrary1DA
damtsImpl.o                   
In file included from core/gfl/gfl_graph_fl.h:16,                                                       
                 from core/GFLLibrary1DAdamtsImpl.cpp:7:                                                
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:448:1: error: template with C linkage
  448 | template<typename __T, omp_allocator_handle_t __Handle>                                     
      | ^~~~~~~~                                                                                        
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here
   10 | extern "C" {                                                                                    
      | ^~~~~~~~~~                                                                                      
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:475:1: error: template with C linkage
  475 | template<typename __T, typename __U, omp_allocator_handle_t __Handle>                       
      | ^~~~~~~~                                                                                        
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here
   10 | extern "C" {                                                                                    
      | ^~~~~~~~~~                
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:483:1: error: template with C linkage
  483 | template<typename __T, omp_allocator_handle_t __Handle,                                     
      | ^~~~~~~~                                                                                        
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here
   10 | extern "C" {                                                                                    
      | ^~~~~~~~~~                                                                                      
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:492:1: error: template with C linkage
  492 | template<typename __T, typename __U, omp_allocator_handle_t __Handle>                           
      | ^~~~~~~~                                   
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here
   10 | extern "C" {                                                                                    
      | ^~~~~~~~~~                                                                                      
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:500:1: error: template with C linkage    
  500 | template<typename __T, omp_allocator_handle_t __Handle,                                         
      | ^~~~~~~~                                                                                        
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here                                                                                                                                           
   10 | extern "C" {                                                                                    
      | ^~~~~~~~~~                            
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:511:1: error: template with C linkage    
  511 | template<typename __T>                                                                          
      | ^~~~~~~~                                                                                        
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here                                   
   10 | extern "C" {                                                                                                                                                                                            
      | ^~~~~~~~~~                                                                                                                                                                                              
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:515:1: error: template with C linkage                                                                                                            
  515 | template<typename __T>                                                                                                                                                                                  
      | ^~~~~~~~              
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here                                   
   10 | extern "C" {                                                                                    
      | ^~~~~~~~~~                                                                                      
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:519:1: error: template with C linkage
  519 | template<typename __T>                                                                          
      | ^~~~~~~~                                                                                        
core/gfl/gfl_graph_fl.h:10:1: note: 'extern "C"' linkage started here                                   
   10 | extern "C" {                                                                                    
      | ^~~~~~~~~~                                                                                      
/opt/conda/lib/gcc/x86_64-conda-linux-gnu/15.1.0/include/omp.h:523:1: error: template with C linkage
  523 | template<typename __T>                                                                          
      | ^~~~~~~~                                                                                            

I'm really not sure how to resolve that. I've added gcc gxx to the installed packages based on googling but I haven't had any success there.

Is there perhaps a dependency that I'm missing?

[hanrong498]

Hi,

I ran into the same problem, and I found a temporary fix (thanks to ChatGPT):

In this file: methylasso-main/src/core/gfl/gfl_graph_fl.h (where the downloaded source code is), I put #include <omp.h> outside of the extern "C" {} block.

Hope this helps!

[abardet]

Thank you so much for the fix! I will also change it in our code. Best, Anaïs

[hexylena]

Hi @abardet I see you closed this but I don't see any changes to the main branch yet, is that expected? Is a new release with this bugfix expected soon? :)

[abardet]

Hi hexylena, I'm traveling at the moment but it's in our to do list, we will test and add this modification latest end of August. Best, Anaïs

[hexylena]

Ah perfect, thank you @abardet !

[abardet]

I just updated the code, thanks @hanrong498

[LiGuangming309]

I just updated the code, thanks [@hanrong498](https://github.com/hanron Hello, an error is still reported in the installation, and the installation cannot be completed.

[LiGuangming309]

make: *** [D:/Rpackages/R-4.5.1/etc/x64/Makeconf:296: difference_detection.o] Error 1
ERROR: compilation failed for package 'MethyLasso'

• removing 'D:/Rpackages/R-4.5.1/library/MethyLasso'
  警告信息:
  In i.p(...) :
  安装程序包‘C:/Users/zhimo/AppData/Local/Temp/RtmpCeZvsW/file7b98225c58f/MethyLasso_1.0.tar.gz’时退出狀態的值不是0

[abardet]

Dear LiGuangming309,
Are you doing the installation using conda? Did you ask an AI to check what could be the error? What OS are you using?
Best, Anaïs

[LiGuangming309]

Dear LiGuangming309, Are you doing the installation using conda? Did you ask an AI to check what could be the error? What OS are you using? Best, Anaïs
n/ld.exe: core/gfl/gfl_utils.o:gfl_utils.c:(.text+0xd22): undefined reference to `gsl_sf_log'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'MethyLasso'

• removing 'C:/Users/zhimo/.conda/envs/MethyLasso/Lib/R/library/MethyLasso' I use conda install the package.

[LiGuangming309]

Thank you very much for your guidance, but I still can't install it here.

[abardet]

Your system is missing the GNU Scientific Library (GSL), which MethyLasso needs. Install the development version of GSL and then reinstall MethyLasso. On Linux/macOS this is straightforward via package managers, on Windows you may need Rtools + a compiled GSL, or use WSL to simplify things.
e.g. sudo apt-get install libgsl-dev