error with gcc command

[Arkadiy-Garber]

Hello,

I am getting the following error when running:

gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h clang: error: cannot specify -o when generating multiple output files

This is after having all the dependencies installed, and doing a manual installation from the source code. As an FYI, in reference to a previous issue, the conda install is not working.

Thanks! Arkadiy

[xiezhq]

Hi Arkadiy,

The reported error is weird. I tested compiling sswlib and it works without error reported. See my screen copy:

[xiezhq@centos7-nat isescan]$ cp -r ssw201507 ~/
[xiezhq@centos7-nat isescan]$ cd
[xiezhq@centos7-nat ~]$ cd ssw201507/
[xiezhq@centos7-nat ssw201507]$ pwd
/home/xiezhq/ssw201507
[xiezhq@centos7-nat ssw201507]$ gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h
[xiezhq@centos7-nat ssw201507]$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[xiezhq@centos7-nat ssw201507]$

What is your OS and gcc version? My OS is centos 7.4 and gcc version is gcc 4.8.5.

Xie

[xiezhq]

Regarding the install with conda, I suggest you have a look at my last answer for the open issue 'ISEScan not available through Bioconda?'. The ISEScan can be installed from conda channel 'conda-forge' as I showed in my that answer, https://github.com/xiezhq/ISEScan/issues/20.

Hope it helps.

Xie