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GregoryFaust / samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
MIT License
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Makefile error OS X #14

Closed LeahRoberts closed 9 years ago

LeahRoberts commented 9 years ago

I'm getting an error when trying to install samblaster. Our IT specialist thinks it could be an OS X compatibility issue as I have an older version of OS X (10.6.8):

g++ -Wall -O3 -D BUILDNUM=21 -c samblaster.cpp -o samblaster.o samblaster.cpp: In function ‘splitLinet* readLine(FILE)’: samblaster.cpp:326: error: ‘getline’ was not declared in this scope make: _\ [samblaster.o] Error 1

Thanks in advance.

GregoryFaust commented 9 years ago

This appears to only occur in OSX installation prior to 10.7 due to the version of the GNU libraries installed. You could try to update to a newer version of the GNU libraries (perhaps dangerous). Alternatively, If I could tell at compile time if getline is or is not supported, then I could supply my own definition. But I don't want to slow down all other runtime configuration with my own potentially slower implementation of getline (The library routine has hopefully been (somewhat) optimized).

LeahRoberts commented 9 years ago

Thanks Greg,

I have updated my workspace to 10.10.3 (Yosemite) which seems to have fixed the problem. Thanks for getting back to me.