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failed to build code #303
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In case it is helpful, FYI: this is caused by a change in autoconf 2.70, which is now the default in homebrew (the only other version available from homebrew now is 2.13; haven't tried that myself). It's fixed in htslib by samtools/htslib#1198 which is released in htslib 1.12. (I happened across this issue while trying to fix it myself, in a different software package) |
Hi, Actually, the same error message still appears even after installing htslib 1.12. Do you have any idea what is being problematic in this case? |
It is an autoconf issue; installing the newest version of htslib will not fix the issue (kallisto comes bundled with an older version of htslib, not htslib 1.12). You need to uninstall autoconf then manually install autoconf 2.69. |
@Yenaled |
It won't work. Kallisto relies on the older version of htslib and I think there are updates in the newer version of htslib that make it incompatible with kallisto. One way is to simply get autoconf 2.69. Otherwise, if you really want to stick with autoconf 2.7, here's a modified version of the installation that should work (at least it does on my end):
Basically, what the above does is add AC_CANONICAL_HOST and AC_PROG_INSTALL to configure.ac and it also runs autoreconf -i (which generates config.guess and config.sub). Credit goes to jmarshall/htslib@16e2301 |
@Yenaled , Thanks. kallisto is now installed in my M1 Mac mini.
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The solution from Jul 22, 2021 works for 0.48.0, but I cannot get it to work on any of the 0.46 versions.
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I have followed https://pachterlab.github.io/kallisto/source guide to build Kallisto on a 11.2.3 macOS Big Sur, doing the following steps:
When I execute % make, I get the following error:
Any idea of what might be going on?
Thank you in advance!
GNU M4 1.4.6
zlib version 1.2.11
cmake version 3.20.1
autoconf version 2.71
hdf5 version 1.12.0_1
g++ version Apple clang version 12.0.0 (clang-1200.0.32.29) Target: x86_64-apple-darwin20.3.0
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