|
From: Colin <col...@gm...> - 2018-06-21 21:02:33
|
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 >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Check out the vibrant tech community on one of the world's most >>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>>> _______________________________________________ >>>>>>> Gmod-ajax mailing list >>>>>>> Gmo...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>> >>>>>> >>>>> >>> > |