STAR compilation error

[aliciachen06]

Discussed in #1503

^{Originally posted by weneuh March 7, 2022}
Hi,
I am getting an error message when trying to compile STAR 2.7.10a on my mac using gcc/11.2.0_3/bin/g++-11:

direct access in function '__ZnamRKSt9nothrow_t.cold' from file '/usr/local/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/x86_64-apple-darwin21/11/../../../libstdc++.a(new_opvnt.o)' to global weak symbol '__ZnamRKSt9nothrow_t' from file '/usr/local/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/x86_64-apple-darwin21/11/../../../libstdc++.a(new_opvnt.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.

here is what I did:

$wget https://github.com/alexdobin/STAR/archive/2.7.10a.tar.gz
$tar -xzf 2.7.10a.tar.gz
$cd STAR-2.7.10a/source
$make STARforMacStatic CXX=/usr/local/Cellar/gcc/11.2.0_3/bin/g++-11

would you have any advice how to resolve this?
many thanks, Werner

STAR compilation error.txt

[aliciachen06]

Need help:

I am using Ubuntu and got the error and terminated at "make STAR". The error message is as follows:
make -C htslib lib-static
make[1]: Entering directory '/home/hchen/STAR-2.7.10a/STAR/source/htslib'
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c
In file included from bgzf.c:38:
htslib/bgzf.h:33:10: fatal error: zlib.h: No such file or directory
33 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make[1]: *** [Makefile:99: bgzf.o] Error 1
make[1]: Leaving directory '/home/hchen/STAR-2.7.10a/STAR/source/htslib'
Makefile:137: Depend.list: No such file or directory
make: *** [Makefile:148: htslib/libhts.a] Error 2

[alexdobin]

Hi @aliciachen06

you need to install zlib library, something like:
$ sudo apt install zlib1g
$ sudo apt install zlib1g-dev

[aliciachen06]

Hi Alex,
It is working now. Thanks.
Alicia

[aliciachen06]

Hi Alex,Is there an updated step by step sample demo on youtube that I can follow? I ran into FATAL ERROR at the first try from one of the related youtube video. Thank you, Alicia On Tuesday, May 24, 2022, 08:56:45 AM PDT, Alexander Dobin ***@***.***> wrote: Closed #1563 as completed. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[alexdobin]

Hi Alicia,

I have not made any youtube videos yet. :)
Please send me the Log.out file of the failed run.

Cheers
Alex

[aliciachen06]

Hi Alex,I don't know where to locate the file/folder I created. Right now I am waiting to increase the memory to my laptop. Will get back to you as soon as I have update. Thank you,Alicia On Thursday, May 26, 2022 at 02:57:33 PM PDT, Alexander Dobin ***@***.***> wrote: Hi Alicia, I have not made any youtube videos yet. :) Please send me the Log.out file of the failed run. Cheers Alex — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>