Re: [Gmod-ajax] request for support

[Colin <col...@gm...>]

I guess I am not sure what to say. If you have zlib-devel it clearly should
not give an error that "zlib.h not found". If you can try a different
system, I would do that. It is not really within the realm of jbrowse to
debug such things.

Note that I did install CentOS 6.9 minimal in a virtualbox and had
JBrowse's setup.sh work fine with the instructions above :)

-Colin

On Thu, Jun 21, 2018 at 6:27 AM Onkar Nath <onk...@gm...> wrote:

> I had updated my system with yum update,
> I tried installing that manually but still the same error comes. I even
> tried forcefully installing but none worked. This same error occurs
> every-time.
>
> --
>
> ONKAR NATH
> Senior Research Fellow
> National Institute of Plant Genome Research
> Aruna Asaf Ali Marg, New Delhi- 110067
> Email- onk...@gm...
> Mob: +91-9136065766
> skype id: onkarnath89
>
>
> On Tue, Jun 19, 2018 at 11:36 AM, Colin <col...@gm...> wrote:
>
>> The steps that are listed have been tested on CentOS 6.9 so it's sort of
>> hard to see what the issue is. You could try manually installing this
>> module to the system with just "cpan PerlIO::gzip" to see what happens
>> Could also try rebooting or yum update? (you didnt include yum update in
>> your list of commands that you replied with)
>>
>>
>>
>> -Colin
>>
>> On Mon, Jun 18, 2018 at 11:33 PM Onkar Nath <onk...@gm...>
>> wrote:
>>
>>> I have tried these and found them installed. I am getting error of
>>> PerlIO::gzip library.
>>>
>>> when installig PerlIO::gzip
>>> error that I get is
>>>
>>> gzip.xs:16:10: fatal error: zlib.h: No such file or directory
>>> #include <zlib.h>
>>> ^~~~~~~~
>>> compilation terminated.
>>> make: *** [gzip.o] Error 1
>>>
>>> I have tried many solutions from web but none of them worked. some of
>>> them are as below:
>>>
>>> *yum install libpng libpng-devel*
>>> Package 2:libpng-1.2.49-2.el6_7.x86_64 already installed and latest
>>> version
>>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and
>>> latest version
>>>
>>> *yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker*
>>>
>>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and
>>> latest version
>>> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest
>>> version
>>> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest
>>> version
>>> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed
>>> and latest version
>>>
>>> *yum groupinstall "Development Tools"*
>>> Package flex-2.5.35-9.el6.x86_64 already installed and latest version
>>> Package gcc-4.4.7-18.el6_9.2.x86_64 already installed and latest version
>>> Package redhat-rpm-config-9.0.3-51.el6.centos.noarch already installed
>>> and latest version
>>> Package rpm-build-4.8.0-55.el6.x86_64 already installed and latest
>>> version
>>> Package 1:make-3.81-23.el6.x86_64 already installed and latest version
>>> Package patch-2.6-8.el6_9.x86_64 already installed and latest version
>>> Package 1:pkgconfig-0.23-9.1.el6.x86_64 already installed and latest
>>> version
>>> Package gettext-0.17-18.el6.x86_64 already installed and latest version
>>> Package automake-1.11.1-4.el6.noarch already installed and latest version
>>> Package bison-2.4.1-5.el6.x86_64 already installed and latest version
>>> Package libtool-2.2.6-15.5.el6.x86_64 already installed and latest
>>> version
>>> Package autoconf-2.63-5.1.el6.noarch already installed and latest version
>>> Package gcc-c++-4.4.7-18.el6_9.2.x86_64 already installed and latest
>>> version
>>> Package binutils-2.20.51.0.2-5.47.el6_9.1.x86_64 already installed and
>>> latest version
>>> Package patchutils-0.3.1-3.1.el6.x86_64 already installed and latest
>>> version
>>> Package byacc-1.9.20070509-7.el6.x86_64 already installed and latest
>>> version
>>> Package indent-2.2.10-7.el6.x86_64 already installed and latest version
>>> Package systemtap-2.9-7.el6.x86_64 already installed and latest version
>>> Package diffstat-1.51-2.el6.x86_64 already installed and latest version
>>> Package elfutils-0.164-2.el6.x86_64 already installed and latest version
>>> Package cvs-1.11.23-16.el6.x86_64 already installed and latest version
>>> Package rcs-5.7-37.el6.x86_64 already installed and latest version
>>> Package subversion-1.6.11-15.el6_7.x86_64 already installed and latest
>>> version
>>> Package gcc-gfortran-4.4.7-18.el6_9.2.x86_64 already installed and
>>> latest version
>>> Package 1:doxygen-1.6.1-6.el6.x86_64 already installed and latest version
>>> Package intltool-0.41.0-1.1.el6.noarch already installed and latest
>>> version
>>> Package git-1.7.1-9.el6_9.x86_64 already installed and latest version
>>> Package ctags-5.8-2.el6.x86_64 already installed and latest version
>>> Package cscope-15.6-7.el6.x86_64 already installed and latest version
>>> Package swig-1.3.40-6.el6.x86_64 already installed and latest version
>>> Warning: Group development does not have any packages.
>>> No packages in any requested group available to install or update
>>>
>>> But Still the error persists.
>>>
>>>
>>>
>>> --
>>>
>>> ONKAR NATH
>>> Senior Research Fellow
>>> National Institute of Plant Genome Research
>>> Aruna Asaf Ali Marg, New Delhi- 110067
>>> Email- onk...@gm...
>>> Mob: +91-9136065766
>>> skype id: onkarnath89
>>>
>>>
>>> On Mon, Jun 18, 2018 at 9:07 PM, Colin <col...@gm...> wrote:
>>>
>>>> Ah ok, centos :)
>>>>
>>>> From this link
>>>> http://www.gmod.org/wiki/JBrowse_Troubleshooting#Linux_-_Red_Hat_.2F_Fedora_.2F_CentOS
>>>>
>>>> I'd recommend
>>>>
>>>> yum update
>>>> yum groupinstall "Development Tools"
>>>> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Mon, Jun 18, 2018 at 1:01 AM Onkar Nath <onk...@gm...>
>>>> wrote:
>>>>
>>>>> I had Ran this command and found all these installed
>>>>>
>>>>> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
>>>>>
>>>>> Details:
>>>>> [root@localhost JBrowse-1.14.2]# yum install libpng-devel gd-devel
>>>>> zlib-devel perl-ExtUtils-MakeMaker
>>>>> Loaded plugins: fastestmirror, refresh-packagekit, security
>>>>> Setting up Install Process
>>>>> Loading mirror speeds from cached hostfile
>>>>>  * base: mirror.dhakacom.com
>>>>>  * epel: ftp.riken.jp
>>>>>  * extras: mirror.dhakacom.com
>>>>>  * updates: mirror.dhakacom.com
>>>>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and
>>>>> latest version
>>>>> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest
>>>>> version
>>>>> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest
>>>>> version
>>>>> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed
>>>>> and latest version
>>>>> Nothing to do
>>>>> [root@localhost JBrowse-1.14.2]#
>>>>>
>>>>> Still this error occurs.
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> ONKAR NATH
>>>>> Senior Research Fellow
>>>>> National Institute of Plant Genome Research
>>>>> Aruna Asaf Ali Marg, New Delhi- 110067
>>>>> Email- onk...@gm...
>>>>> Mob: +91-9136065766
>>>>> skype id: onkarnath89
>>>>>
>>>>>
>>>>> On Sun, Jun 17, 2018 at 5:54 AM, Colin <col...@gm...> wrote:
>>>>>
>>>>>> It is recommended to install zlib and some basic dependencies for
>>>>>> your linux setup
>>>>>>
>>>>>> A command you can run is here
>>>>>>
>>>>>> http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse
>>>>>>
>>>>>>
>>>>>>  sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev
>>>>>> build-essential
>>>>>>
>>>>>>
>>>>>> -Colin
>>>>>>
>>>>>> On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> Dear JBrowse team,
>>>>>>> I want to imbed JBrowse into my html page. So I tried installing it
>>>>>>> on my system. But I am getting an error of zlib.h. I have tried the
>>>>>>> instructions available on your wikipage and some others by google search.
>>>>>>> But none has worked. Kindly Consider the related log file.
>>>>>>> Any support will be helpful.
>>>>>>> Waiting eagerly for your reply.
>>>>>>>
>>>>>>> Regards
>>>>>>> --
>>>>>>>
>>>>>>> ONKAR NATH
>>>>>>> Senior Research Fellow
>>>>>>> National Institute of Plant Genome Research
>>>>>>> Aruna Asaf Ali Marg, New Delhi- 110067
>>>>>>> Email- onk...@gm...
>>>>>>> Mob: +91-9136065766
>>>>>>> skype id: onkarnath89
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
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>>>>>>> _______________________________________________
>>>>>>> Gmod-ajax mailing list
>>>>>>> Gmo...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>>
>>>>>>
>>>>>
>>>
>