I tried to compile HMMER v3.2.1 in Cygwin using


followed by



make install

but failed. I got this config.log file to troubleshoot and I suspect the solution is in this line:

configure:2908: error: no acceptable C compiler found in $PATH

What does it mean? Is it really all I need to address? I followed the installation steps in this document.


1 Answer 1


I would strongly recommend to use Bioconda instead of compiling. It is one of the channels ("distributors of packages") in Anaconda Cloud which is basically a package source for conda.

In short - conda allows you to create virtual environments isolated from system and to install various precompiled software packages with one command (so, by the way, you can easily use multiple software versions on one system). Also, Bioconda is just one channel aiming on various bioinformatics software, but many more packages can be found in aforementioned Anaconda Cloud.

Tutorial how to start using Bioconda is on its homepage, and it is really easy (far more easier than to struggle with compiling).

Bioconda HMMER package

P.S. Of course there are cases in which you need a specific build of given software. Than it is really needed to compile manually.

  • $\begingroup$ Thank you. The website says "Bioconda supports only 64-bit Linux and Mac OSX." I am a Windows user, so I assume I will need to go back to compiling. Bioconda sounds amazing though; thanks for bringing it to my/our attention. $\endgroup$
    – JernejT
    Nov 16, 2018 at 3:53
  • $\begingroup$ I tried to set up channels with conda config --add channels defaults, conda config --add channels bioconda & conda config --add channels conda-forge in my Anaconda prompt which seemingly worked, but conda install hmmer didn't. $\endgroup$
    – JernejT
    Nov 16, 2018 at 4:29
  • $\begingroup$ @JernejT On Windows? And what does conda install hmmer output? Anyway, Linux is much more supported platform for bioinformatics. Worth to try :) $\endgroup$
    – jirinovo
    Nov 16, 2018 at 10:54

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.