Re: [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1

[VIB | Stephane Plaisance]

Thanks Robert for the rapid feedback, I tried but it die not fix it. I seem to have an issue with gcc I did install Xcode and the cl-tools though ! xcode-select --install xcode-select: error: command line tools are already installed, use "Software Update" to install updates Attached the failure report for the build This is a computer freshly clean-installed with high Sierra and Xcode from the apple store

config.log
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Stephane Plaisance, Ph.D Address: Herestraat 49, O&N4, Post Box 816, Room nr. 404-24 / 08.428, 3000 Leuven - Belgium Tel: +32 (0)16 37 31 26 Lync: +32 (0)16 32 00 60 Fax: +32 (0)16 37 31 29 Web: www.nucleomics.be On 17 Nov 2017, at 18:03, Robert Davies <r...@sanger.ac.uk> wrote: On Fri, 17 Nov 2017, VIB | Stephane Plaisance wrote: I did install before but after upgrading to high Sierra I am lacking some dev dependencies (Xcode is installed) I tried installing xz using macport and got the error below (there is no port with -dev) xz -V xz (XZ Utils) 5.2.3 liblzma 5.2.3 I haven't really tried macports myself so this is a bit of a guess, but here goes... Having looked at the macports documentation and the configure output below it looks like macports doesn't install the 'lzma.h' header file in a location where it would normally be found.  You can fix this by giving configure a hint to say where it is. Try running 'port contents xz', which should list all the files installed for the xz package.  The list should include something like: /opt/local/include/lzma.h In which case running configure like this should fix the problem: ./configure CPPFLAGS='/opt/local/include' From the configure output, it looks like it's finding the library so hopefully this is all you need.  If configure works, you should be able to build the package with 'make' as normal. Please give this a try and let us know if it works. I then found a post by schneidexe <https://github.com/schneidexe> https://github.com/sparklemotion/nokogiri/issues/1483 <https://github.com/sparklemotion/nokogiri/issues/1483> to build zx from source and did it This seems to be someone using homebrew, so not really relevant to your problem.  Building samtools and htslib with homebrew does work, as this is the way that it gets tested on MacOS. => same error I do not find a lilzma-dev for OSX 10.13.1 and do not use brew on my Mac (macport only) Thanks for any suggestion Stephane checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... no checking for lzma_easy_buffer_encode in -llzma... yes configure: error: liblzma development files not found The CRAM format may use LZMA2 compression, which is implemented in HTSlib by using compression routines from liblzma <http://tukaani.org/xz/>. Building HTSlib requires liblzma development files to be installed on the build machine; you may need to ensure a package such as liblzma-dev (on Debian or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or xz (via Homebrew on macOS) is installed; or build XZ Utils from source. Either configure with --disable-lzma (which will make some CRAM files produced elsewhere unreadable) or resolve this error to build HTSlib. configure: error: ./configure failed for htslib-1.6 <http://www.nucleomics.be/>       Stephane Plaisance, Ph.D Rob Davies              r...@sanger.ac.uk The Sanger Institute    http://www.sanger.ac.uk/ Hinxton, Cambs.,        Tel. +44 (1223) 834244 CB10 1SA, U.K.          Fax. +44 (1223) 494919 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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