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Installation error in make process #28
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Hi,
There are static bins and a docker available.
Try to use them, no need to recompile.
Best,
O
Le mar. 25 avr. 2023, 06:16, BIOJHK ***@***.***> a écrit :
… Hello, I used shapeit4 in last year, but I want to use shapeit5 also.
When I do shapeit5 installation process, fatal error popped up and
cosuming my time...
I'm working with this version,
(base) ***@***.***:~/Public/230424/shapeit5/phase_rare$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
and Centos also. (I will install Centos later when this error solved and
successfully installed.)
Make error occurred here..
/home/jhk0709/Public/230424/htslib/hfile_s3_write.c:859: undefined
reference to curl_global_init' /usr/bin/ld:
/home/jhk0709/Public/230424/htslib/hfile_s3_write.c:866: undefined
reference to curl_share_init'
/usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:874:
undefined reference to curl_share_setopt' /usr/bin/ld:
/home/jhk0709/Public/230424/htslib/hfile_s3_write.c:875: undefined
reference to curl_share_setopt'
/usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:876:
undefined reference to curl_share_setopt' /usr/bin/ld:
/home/jhk0709/Public/230424/htslib/hfile_s3_write.c:885: undefined
reference to curl_version_info'
/usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:879:
undefined reference to curl_share_cleanup' /usr/bin/ld:
/home/jhk0709/Public/230424/htslib/hfile_s3_write.c:880: undefined
reference to curl_global_cleanup'
/usr/bin/ld: /usr/local/lib/libhts.a(hfile_s3_write.o): in function s3_write_exit':
/home/jhk0709/Public/230424/htslib/hfile_s3_write.c:831: undefined
reference to curl_global_cleanup'
collect2: error: ld returned 1 exit status
make: *** [makefile:129: bin/phase_rare] Error 1
when I install with htslib, it doesn't process well so I check link all *c
file - and same error message popped up!
(base) ***@***.***:~/Public/230424/htslib-1.17$ gcc hfile_s3_write.c
-lcurl
hfile_s3_write.c:67:10: fatal error: config.h: No such file or directory
67 | #include <config.h>
| ^~~~~~~~~~
compilation terminated.
when I found the message for your installation guide, when the htslib
successfully done with make process,
it has no libhts.a (so I make link with ln -s to /usr/local/lib/)
and CPATH to solve htslib and samtools.
What can I do for solve this make solution?
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Oh, thank you for quick reply! (base) jhk0709@R750xs:~/Public/230424/shapeit5-5.1.0/phase_common$ ls bin/ (base) jhk0709@R750xs:~/Public/230424/shapeit5-5.1.0/phase_common$ ls obj/ (base) jhk0709@R750xs:~/Public/230424/shapeit5-5.1.0/phase_common$ ls src/ Is it right that I just download and using shapeit5 immediately? and I remember in shapeit4, installation process is need to write path for confirmmation(is it right? I can't remember exact words) like, but in shapeit5 guide to do just 'make'. Thank you. |
Oops. I found the solution. If i do shapeit5 in linux environments, ex)
Thank you. |
Just download the static binaries in the v5.1.1 pre-release. |
Oh, thank you for updated information. I just downloaded and check the program works well. |
Hello, I used shapeit4 in last year, but I want to use shapeit5 also.
When I do shapeit5 installation process, fatal error popped up and cosuming my time...
I'm working with this version,
(base) jhk0709@R750xs:~/Public/230424/shapeit5/phase_rare$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
and Centos also. (I will install shapeit5 in Centos later when this error solved and successfully installed.)
Make error occurred here..
/home/jhk0709/Public/230424/htslib/hfile_s3_write.c:859: undefined reference to
curl_global_init' /usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:866: undefined reference to
curl_share_init'/usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:874: undefined reference to
curl_share_setopt' /usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:875: undefined reference to
curl_share_setopt'/usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:876: undefined reference to
curl_share_setopt' /usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:885: undefined reference to
curl_version_info'/usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:879: undefined reference to
curl_share_cleanup' /usr/bin/ld: /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:880: undefined reference to
curl_global_cleanup'/usr/bin/ld: /usr/local/lib/libhts.a(hfile_s3_write.o): in function
s3_write_exit': /home/jhk0709/Public/230424/htslib/hfile_s3_write.c:831: undefined reference to
curl_global_cleanup'collect2: error: ld returned 1 exit status
make: *** [makefile:129: bin/phase_rare] Error 1
when I install with htslib, it doesn't process well so I check link all *c file - and same error message popped up!
(base) jhk0709@R750xs:~/Public/230424/htslib-1.17$ gcc hfile_s3_write.c -lcurl
hfile_s3_write.c:67:10: fatal error: config.h: No such file or directory
67 | #include <config.h>
| ^~~~~~~~~~
compilation terminated.
when I found the message for your installation guide, when the htslib successfully done with make process,
it has no libhts.a (so I make link with ln -s to /usr/local/lib/)
and CPATH to solve htslib and samtools.
What can I do for solve this make solution?
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