getting several install errors about gembs

[heathsc]

Thank you for the report. We'll look into this and get back to you. Simon

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On 17 Oct 2017 9:08 am, "Christa Caggiano" ***@***.***> wrote: Hi, I was really enthusiastic about your new bioarvix paper! Upon installing I am getting several errors when I try to run python setup.py install --user. Most of these errors seem to be related to bs_call.c s_call.c:284: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘*attribute*’ before ‘ *’ token bs_call.c:357: error: expected ‘)’ before ‘*’ token bs_call.c:373: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘*attribute*’ before ‘*’ token bs_call.c: In function ‘do_calling’: bs_call.c:417: error: ‘gsl_integration_glfixed_table’ undeclared (first use in this function) bs_call.c:417: error: (Each undeclared identifier is reported only once bs_call.c:417: error: for each function it appears in.) bs_call.c:417: error: ‘tab1’ undeclared (first use in this function) bs_call.c:417: error: ‘tab2’ undeclared (first use in this function) bs_call.c:417: warning: left-hand operand of comma expression has no effect bs_call.c:420: warning: implicit declaration of function ‘get_gl_tab’ bs_call.c: In function ‘call_genotypes_ML’: bs_call.c:1485: warning: array subscript has type ‘char’ bs_call.c:1433: warning: unused variable ‘fisher_p’ bs_call.c:1432: warning: unused variable ‘nr’ I am using python 2.6.6 as per the instructions. I think I have properly configured gsl-2.4 according to the gsl website instructions, however, I was unsure of the difference between include and lib so that could be a potential source of c related error. Any advice you would have here is greatly appreciated! Thanks, Christa — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdyYQ9a36fBONtxo4PcDaPXtQoQIlks5stFJdgaJpZM4P7rPL> .

[MarcosFernandez]

Hi Christa,

Thanks a lot for your interest on gemBS.
I guess your problem is that you have to fix the file Gsl.mk with the proper GSL paths.
This file is found at:

gemBS/tools/bs_call/

And you must modify two lines:
GSL_LIB = -L/yourGSLinstallation/lib/
GSL_INC = -I/yourGSLinstallation/include/

Once modified try to repeat the installation process.