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Oshlack / Corset

Software for clustering de novo assembled transcripts and counting overlapping reads
https://github.com/Oshlack/Corset/wiki
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error compiling from source #13

Closed stuartwillis closed 5 years ago

stuartwillis commented 7 years ago

I received an error trying to make from source on SL7. gcc is 4.8.5-11.el7. Here's the output:

[root@earth Corset-version-1.06]# make g++ -I/samtools-1.3.1/htslib-1.3.1 -I/samtools-1.3.1 -O3 -ffast-math -I./ -std=c++0x -DUNORDEREDMAP corset.o Cluster.o MakeClusters.o Transcript.o Read.o -o corset -L/samtools-1.3.1 -lpthread -lbam -lz /samtools-1.3.1/htslib-1.3.1/libhts.a Transcript.o: file not recognized: File format not recognized collect2: error: ld returned 1 exit status make: *** [corset] Error 1

Not sure what to make of that, except that Transcripts.o is obviously a Corset file. Noticed that configure gave the following warnings too:

configure: WARNING: bam.h: accepted by the compiler, rejected by the preprocessor! configure: WARNING: bam.h: proceeding with the compiler's result ... configure: WARNING: sam.h: accepted by the compiler, rejected by the preprocessor! configure: WARNING: sam.h: proceeding with the compiler's result

Tried both samtools 1.3.1 and 1.4.1. The pre-compiled version seems to work but in general I prefer to compile locally. Any suggestions?