failed to build code

[FabianaRossi]

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:

# install Homebrew package manager
   % /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

   # use homebrew to install cmake, autoconf, HDF5 library
   % brew install cmake
   % brew install autoconf
   % brew install hdf5

   # get the kallisto source code, unpack, build, and install it:

   % git clone https://github.com/pachterlab/kallisto.git
   % cd kallisto
   % cd ext/htslib
   % autoheader
   % autoconf
   % cd ../..
   % mkdir build
   % cd build
   % cmake ..
   % make
   % make install

When I execute % make, I get the following error:

[  3%] Creating directories for 'htslib'
[  6%] No download step for 'htslib'
[ 10%] No update step for 'htslib'
[ 13%] No patch step for 'htslib'
[ 17%] Performing configure step for 'htslib'
configure: error: cannot find required auxiliary files: config.guess config.sub
make[2]: *** [../ext/htslib/src/htslib-stamp/htslib-configure] Error 1
make[1]: *** [CMakeFiles/htslib.dir/all] Error 2
make: *** [all] Error 2

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

[ihnorton]

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 https://github.com/samtools/htslib/pull/1198 which is released in htslib 1.12. (I happened across this issue while trying to fix it myself, in a different software package)

[t4eyang]

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? I am quite new to git and it is bit confusing in terms of where I should be starting

[Yenaled]

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.

[akhst7]

@Yenaled I have a htslib 1.13 installed by brew. Is there any way to skip htslib config step by providing the path to existing htslib 1.13 during make process ?

[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):

git clone https://github.com/pachterlab/kallisto.git
cd kallisto/ext/htslib
sed '/AC_PROG_CC/a \
AC_CANONICAL_HOST \
AC_PROG_INSTALL \
' configure.ac > configure.ac2
mv configure.ac2 configure.ac
autoreconf -i
autoheader
autoconf
cd ../../
mkdir build
cd build
cmake ..
make
make install

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 https://github.com/jmarshall/htslib/commit/16e2301c62ac6bf32ddcaf96c112f09bd045d47b

[akhst7]

@Yenaled , Thanks. kallisto is now installed in my M1 Mac mini.

build git:(master) ✗ sudo make install
Password:
[ 27%] Built target htslib
[ 93%] Built target kallisto_core
[100%] Built target kallisto
Install the project...
-- Install configuration: "Release"
-- Installing: /usr/local/bin/kallisto

autoconf -V
autoconf (GNU Autoconf) 2.71
Copyright (C) 2021 Free Software Foundation, Inc.
License GPLv3+/Autoconf: GNU GPL version 3 or later
<https://gnu.org/licenses/gpl.html>, <https://gnu.org/licenses/exceptions.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by David J. MacKenzie and Akim Demaille.

 ~ neofetch
                 ,xNMM.          -------------------------
               .OMMMMo           OS: macOS 11.5.1 20G80 arm64
               OMMM0,            Host: Macmini9,1
     .;loddo:' loolloddol;.      Kernel: 20.6.0
   cKMMMMMMMMMMNWMMMMMMMMMM0:    Uptime: 5 days, 21 hours, 58 mins
 .KMMMMMMMMMMMMMMMMMMMMMMMWd.    Packages: 70 (brew)
 XMMMMMMMMMMMMMMMMMMMMMMMX.      Shell: zsh 5.8
;MMMMMMMMMMMMMMMMMMMMMMMM:       Resolution: 1920x1080
:MMMMMMMMMMMMMMMMMMMMMMMM:       DE: Aqua
.MMMMMMMMMMMMMMMMMMMMMMMMX.      WM: Quartz Compositor
 kMMMMMMMMMMMMMMMMMMMMMMMMWd.    WM Theme: Blue (Light)
 .XMMMMMMMMMMMMMMMMMMMMMMMMMMk   Terminal: iTerm2
  .XMMMMMMMMMMMMMMMMMMMMMMMMK.   Terminal Font: Monaco 11
    kMMMMMMMMMMMMMMMMMMMMMMd     CPU: Apple M1
     ;KMMMMMMMWXXWMMMMMMMk.      GPU: Apple M1
       .cooc,.    .,coo:.        Memory: 2376MiB / 16384MiB

~ kallisto
kallisto 0.46.2

Usage: kallisto <CMD> [arguments] ..

Where <CMD> can be one of:

    index         Builds a kallisto index
    quant         Runs the quantification algorithm
    bus           Generate BUS files for single-cell data
    pseudo        Runs the pseudoalignment step
    merge         Merges several batch runs
    h5dump        Converts HDF5-formatted results to plaintext
    inspect       Inspects and gives information about an index
    version       Prints version information
    cite          Prints citation information

Running kallisto <CMD> without arguments prints usage information for <CMD>

[stiv1n]

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. I am using the htslib provided in the source folders.

[ 62%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o
/src/MinCollector.cpp: In member function ‘std::vector<int> MinCollector::intersectECs(std::vector<std::pair<KmerEntry, int> >&) const’:
/src/MinCollector.cpp:194:21: error: ‘numeric_limits’ is not a member of ‘std’
  194 |   int minpos = std::numeric_limits<int>::max();
      |                     ^~~~~~~~~~~~~~
/src/MinCollector.cpp:194:36: error: expected primary-expression before ‘int’
  194 |   int minpos = std::numeric_limits<int>::max();
      |                                    ^~~
/src/MinCollector.cpp: In member function ‘double MinCollector::get_mean_frag_len(bool) const’:
src/MinCollector.cpp:294:19: error: ‘numeric_limits’ is not a member of ‘std’
  294 |       return std::numeric_limits<double>::max();
      |                   ^~~~~~~~~~~~~~
/src/MinCollector.cpp:294:34: error: expected primary-expression before ‘double’
  294 |       return std::numeric_limits<double>::max();
      |                                  ^~~~~~
/src/MinCollector.cpp:294:34: error: expected ‘;’ before ‘double’
  294 |       return std::numeric_limits<double>::max();
      |                                  ^~~~~~
      |                                  ;
/src/MinCollector.cpp:294:40: error: expected unqualified-id before ‘>’ token
  294 |       return std::numeric_limits<double>::max();
      |                                        ^
make[2]: *** [src/CMakeFiles/kallisto_core.dir/build.make:202: src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:128: src/CMakeFiles/kallisto_core.dir/all] Error 2
make: *** [Makefile:136: all] Error 2