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qmarcou / IGoR

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:
https://qmarcou.github.io/IGoR/
GNU General Public License v3.0
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Install error #64

Closed shwdmsh closed 3 years ago

shwdmsh commented 3 years ago

Hi,I use these commans as follows to install IGoR ,some error as follows:

include/jemalloc/internal/../jemalloc.h:59:28: error: redefinition of 'aligned_alloc'

define je_aligned_alloc aligned_alloc

                        ^

src/jemalloc.c:1978:1: note: in expansion of macro 'je_aligned_alloc' je_aligned_alloc(size_t alignment, size_t size) { ^~~~ In file included from include/jemalloc/internal/jemalloc_internal_decls.h:50:0, from include/jemalloc/internal/jemalloc_preamble.h:5, from src/jemalloc.c:2: /root/anaconda3/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/stdlib.h:513:21: note: previous definition of 'aligned_alloc' was here static inline void* aligned_alloc (size_t al, size_t sz)

Could you help me ? My centos version is 7.0. Then: ./configure make(some error)

qmarcou commented 3 years ago

Dear @shwdmsh It seems you have a conflict with some anaconda C library, however I would need more information to give you some hints. As it seems you have closed this issue, I guess you found a solution to your problem, could you please write it up here or give hints of the nature of the problem and solutions for other users bumping into this? Best regards

shwdmsh commented 3 years ago

Dear Sir/Madam,

Thank you very much for help! I have another question. When I use the command as follows,I can get the full results: igor -set_wd $WDPATH -batch foo -species human -chain IGL -align However,I use the command : igor -set_wd $WDPATH -batch foo -species human -chain IGL -align ---best_align_only ---best_gene_only some errors showing: [IGoR] ERROR: Unknown gene specification"---best_align_only"for -align [IGoR] ERROR: Use "man igor", "igor -help" or visit https://github.com/qmarcou/IGoR to see available commands and their effects. How can I get the best align only and the best gene only result? Thank you for your help!

Best regards

At 2021-07-21 17:46:26, "qmarcou" @.***> wrote:

Dear @shwdmsh It seems you have a conflict with some anaconda C library, however I would need more information to give you some hints. As it seems you have closed this issue, I guess you found a solution to your problem, could you please write it up here or give hints of the nature of the problem and solutions for other users bumping into this? Best regards

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