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jfarek / xatlas

BSD 3-Clause "New" or "Revised" License
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installation error #1

Open goldenflaw opened 6 years ago

goldenflaw commented 6 years ago

Hello,

I would like to try your tool, but I ran into installation problems. I have htslib/1.4.1, but here is the error I got:

Xatlas.cpp:864:23: error: request for member ‘second’ in ‘coord’, which is of non-class type ‘const int’ if (coord.second > max_len) { ^ Xatlas.cpp:865:33: error: request for member ‘second’ in ‘coord’, which is of non-class type ‘const int’ max_len = coord.second; ^ Xatlas.cpp:877:10: error: ‘args_s’ has no member named ‘min_indel_mapq’ args.min_indel_mapq = min_indel_mapq; ^ Xatlas.cpp:878:10: error: ‘args_s’ has no member named ‘min_snp_mapq’ args.min_snp_mapq = min_snp_mapq; ^ Xatlas.cpp:889:30: error: ‘opts_s’ has no member named ‘snp_near_end_bases’ EventScanner events(opts.snp_near_end_bases, snp_max_sub, snp_max_indel); ^ make: *** [Xatlas.o] Error 1

philippbayer commented 6 years ago

I've just run into the same error - in my case on my cluster, a very old gcc was the default (4.8.5). After switching to a more recent gcc (7.2.0) via module load, make runs through fine.

jfarek commented 6 years ago

Hi,

xAtlas requires compiler support for C++11. I've been able to build xAtlas using GCC 4.9.4 and 5.4.0 on our cluster, so these versions or anything newer should provide C++11 support. I'll update the autoconf script to add a check for this when running configure.