[Bio-Linux] FW: [Bio-linux-announce] Bio-Linux 8 now available
Tauqeer Alam
tauqeer9 at gmail.com
Sun Aug 3 01:55:01 EDT 2014
Hi All
I am trying to reinstall Parallels Tools ('cd /media/Parallels\ Tools/'
followed by 'sudo ./install) but getting following error. I would really
appreciate if somebody help me resolve this problem. Eventually I want to
upgrade to Biolinux8.
Thanks
Tauqeer
2014-08-03T01:14:11-0400: execCmd: ./install --install [143]
2014-08-03T01:14:11-0400: Error: An error occurred when installing
Parallels Tools. Please go to /var/log/parallels-tools-install.log for more
information.
2014-08-03T01:14:15-0400: Exiting with code 1
2014-08-03T01:14:31-0400: Exiting with code 1
2014-08-03T01:30:07-0400:
Parallels Tools 8.0.18619.1001606 Installer started.
2014-08-03T01:30:17-0400: execCmd: ./installer/pm.sh check_guest_tools 2>&1
[0]
Sun Aug 3 01:30:17 EDT 2014
Start installation or upgrade of Guest Tools
new version of parallels tools
Installed Guest Tools were not found
Perform installation into the /usr/lib/parallels-tools directory
cat: /usr/lib/parallels-tools/kmods/../version: No such file or directory
Start installation of prl_eth kernel module
make: Entering directory `/usr/lib/parallels-tools/kmods'
cd prl_eth/pvmnet && make
make[1]: Entering directory `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet'
make -C /lib/modules/3.13.0-32-generic/build
M=/usr/lib/parallels-tools/kmods/prl_eth/pvmnet
make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic'
LD /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/built-in.o
CC [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/pvmnet.o
LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.o
Building modules, stage 2.
MODPOST 1 modules
CC /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.mod.o
LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.ko
make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic'
make[1]: Leaving directory `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet'
cd prl_tg/Toolgate/Guest/Linux/prl_tg && make
make[1]: Entering directory
`/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg'
make -C /lib/modules/3.13.0-32-generic/build
SUBDIRS=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg
SRCROOT=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg
modules
make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic'
CC [M]
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:
In function ‘prl_tg_write’:
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:9:
error: implicit declaration of function ‘PDE’
[-Werror=implicit-function-declaration]
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:31:
error: invalid type argument of ‘->’ (have ‘int’)
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:
In function ‘prl_tg_init_one’:
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:2:
error: implicit declaration of function ‘create_proc_entry’
[-Werror=implicit-function-declaration]
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:4:
warning: assignment makes pointer from integer without a cast [enabled by
default]
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1305:4:
error: dereferencing pointer to incomplete type
/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1306:4:
error: dereferencing pointer to incomplete type
cc1: some warnings being treated as errors
make[3]: ***
[/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o]
Error 1
make[2]: ***
[_module_/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg]
Error 2
make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic'
make[1]: *** [prl_tg] Error 2
make[1]: Leaving directory
`/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg'
make: *** [installme] Error 2
make: Leaving directory `/usr/lib/parallels-tools/kmods'
Error: could not build kernel modules
Error: failed to install kernel modules
On Sun, Aug 3, 2014 at 1:40 AM, Tauqeer Alam <tauqeer9 at gmail.com> wrote:
> Hi All
> I am trying to reinstall Parallels Tools ('cd /media/Parallels\ Tools/'
> followed by 'sudo ./install) but getting following error. I would really
> appreciate if somebody help me resolve this problem. Eventually I want to
> upgrade to Biolinux8.
>
> Thanks
>
> Tauqeer
>
>
> On Sat, Aug 2, 2014 at 2:57 PM, Stephen P. Molnar <s.molnar at sbcglobal.net>
> wrote:
>
>> Please see the following messages.
>>
>>
>>
>> Thanks in advance.
>>
>>
>>
>> Stephen P. Molnar, Ph.D. Life is a
>> fuzzy set
>>
>> Foundation for Chemistry Stochastic and
>> multivariate
>>
>> www.FoundationForChemistry.com
>>
>> (614)312-7528 (c)
>>
>> Skype: smolnar1
>>
>>
>>
>>
>>
>> -----Original Message-----
>>
>> From: Tim Booth [mailto:tbooth at ceh.ac.uk <tbooth at ceh.ac.uk>]
>>
>> Sent: Friday, August 01, 2014 9:40 AM
>>
>> To: Stephen P. Molnar
>>
>> Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available
>>
>>
>>
>> Hi Stephen,
>>
>>
>>
>> Glad you sorted out the shell.
>>
>>
>>
>> I'm sorry, but I can't say what might be up with the keyboard and I'm not
>> going to start experimenting with XFCE right now as I have other
>> priorities. You may well have more luck on the discussion mailing list:
>>
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>>
>>
>>
>> Cheers,
>>
>>
>>
>> TIM
>>
>>
>>
>> On Fri, 2014-08-01 at 11:59 +0100, Stephen P. Molnar wrote:
>>
>> > Thanks for the reply. As it turns out that was a red-faced forehead
>>
>> > slapping problem. After dispatching my note I realized that the shell
>>
>> > was zsh.
>>
>> >
>>
>> > Thanks to your reply I have successfully changed the default shell to
>>
>> > bash.
>>
>> >
>>
>> > There is, however anew problem, also a head scratcher for me. As I
>>
>> > don't like the Gnome shell and had become unenchanted with KDE, my
>>
>> > desktop of choice on my linux machines is XFCE, with Xfe as the file
>>
>> > manager of choice. I find that the keyboard doesn't seem to be
>>
>> > recognized by the xfwrite editor. On the other hand, nedit works as it
>>
>> > should.
>>
>> >
>>
>> > Your input about this problem would be much appreciated.
>>
>> >
>>
>> > Thanks in advance.
>>
>> >
>>
>> > Stephen P. Molnar, Ph.D. Life is a
>> fuzzy set
>>
>> > Foundation for Chemistry Stochastic
>> and multivariate
>>
>> > www.FoundationForChemistry.com
>>
>> > (614)312-7528 (c)
>>
>> > Skype: smolnar1
>>
>> >
>>
>> >
>>
>> > -----Original Message-----
>>
>> > From: Tim Booth [mailto:tbooth at ceh.ac.uk <tbooth at ceh.ac.uk>]
>>
>> > Sent: Friday, August 01, 2014 5:05 AM
>>
>> > To: Stephen P. Molnar
>>
>> > Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available
>>
>> >
>>
>> > Hi Stephen,
>>
>> >
>>
>> > Nothing so mysterious here. The default shell on Bio-Linux is ZSH, so
>> if you are a BASH fan you'll want to do:
>>
>> >
>>
>> > chsh -s /bin/bash
>>
>> > exec bash -l
>>
>> >
>>
>> > We do already have both L and ll aliased to that command, but not "l"
>>
>> > :-)
>>
>> >
>>
>> > Cheers,
>>
>> >
>>
>> > TIM
>>
>> >
>>
>> > On Thu, 2014-07-31 at 20:16 +0100, Stephen P. Molnar wrote:
>>
>> > > I have encountered a rather strange problem with the new BioLinux v
>>
>> > > 8 latest.
>>
>> > >
>>
>> > > I installed the distribution in a VMware Player without any problems
>>
>> > > or error messages. In fact, I have a Debian v-7.6.0 distribution
>>
>> > > running in the same VMware device. Consequently, I have confidence
>>
>> > > in the virtual computer and my laptop on which it is running.
>>
>> > >
>>
>> > > I edited .bashrc to include the line alias l='ls -l --color'
>>
>> > >
>>
>> > > When I source the edited .bashrc file I get the following:
>>
>> > >
>>
>> > > computation at inga[computation] source
>> .bashrc [
>>
>> > > 2:57PM]
>>
>> > > .bashrc:16: command not found: shopt
>>
>> > > .bashrc:24: command not found: shopt
>>
>> > > .bashrc:108: command not found: shopt
>>
>> > > /usr/share/bash-completion/bash_completion:35: parse error near `]]'
>>
>> > > \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$
>> [
>>
>> > > 2:57PM]
>>
>> > >
>>
>> > > The problem seems to be that shopt is missing!
>>
>> > >
>>
>> > > Please advise.
>>
>> > >
>>
>> > > Thanks in advance.
>>
>> > >
>>
>> > > Stephen P. Molnar, Ph.D. Life is a
>> fuzzy
>>
>> > > set
>>
>> > > Foundation for Chemistry Stochastic
>> and
>>
>> > > multivariate
>>
>> > > www.FoundationForChemistry.com
>>
>> > > (614)312-7528 (c)
>>
>> > > Skype: smolnar1
>>
>> > >
>>
>> > > -----Original Message-----
>>
>> > > From: Tim Booth [mailto:tbooth at ceh.ac.uk <tbooth at ceh.ac.uk>]
>>
>> > > Sent: Wednesday, July 30, 2014 11:55 AM
>>
>> > > To: bio-linux-announce at nebclists.nerc.ac.uk; Bio-Linux mailing list
>>
>> > > Subject: [Bio-linux-announce] Bio-Linux 8 now available
>>
>> > >
>>
>> > > Dear All,
>>
>> > >
>>
>> > > The Bio-Linux system gets a major new release every two years
>>
>> > > following the regular Ubuntu "LTS" releases. Since Ubuntu 14.04 LTS
>>
>> > > came out in April I've been working with help from the Bio-Linux
>>
>> > > community to make Bio-Linux 8 and it is now ready and available via
>> the new website.
>>
>> > >
>>
>> > > http://environmentalomics.org/bio-linux/
>>
>> > >
>>
>> > > Upgrades from Bio-Linux 7 to 8 do not require re-installation. I
>>
>> > > encourage you all to upgrade soon, as new bioinformatics packages
>>
>> > > will no longer be provided for Bio-Linux 7. See the "Installation"
>>
>> > > section for instructions on upgrading your BL7 machine.
>>
>> > >
>>
>> > > The new Ubuntu 14.04 base system brings many benefits such as
>>
>> > > increased hardware compatibility and new office and multimedia
>>
>> > > software, but Bio-Linux itself also has many improvements and
>> new/updated packages.
>>
>> > > Also for the first time there is a version in OVA format for
>>
>> > > VirtualBox/VMWare users, and this version will be updated whenever
>>
>> > > new ISO files are released. See the "What's New" and "Software List"
>>
>> > > pages on the website for details.
>>
>> > >
>>
>> > > As ever, please report problems and feedback to
>>
>> > > helpdesk at nebc.nerc.ac.uk. I can't promise to fix everything but
>>
>> > > will endeavour to provide help and squash bugs where I can. Also,
>>
>> > > please let me know if you use Bio-Linux for teaching or manage a
>>
>> > > large installation on your departmental server or computing lab.
>>
>> > > The more we can prove that people find this stuff useful, the more
>> likely we are to get future funding!
>>
>> > >
>>
>> > > I hope you enjoy using Bio-Linux 8.
>>
>> > >
>>
>> > > TIM
>>
>> > >
>>
>> > > --
>>
>> > > Tim Booth <tbooth at ceh.ac.uk>
>>
>> > > NERC Environmental Bioinformatics Centre
>>
>> > >
>>
>> > > Centre for Ecology and Hydrology
>>
>> > > Maclean Bldg, Benson Lane
>>
>> > > Crowmarsh Gifford
>>
>> > > Wallingford, England
>>
>> > > OX10 8BB
>>
>> > >
>>
>> > > http://nebc.nerc.ac.uk
>>
>> > > +44 1491 69 2705
>>
>> > > _______________________________________________
>>
>> > > Bio-Linux-announce mailing list
>>
>> > > Bio-Linux-announce at nebclists.nerc.ac.uk
>>
>> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-announce
>>
>> > >
>>
>> >
>>
>> > --
>>
>> > Tim Booth <tbooth at ceh.ac.uk>
>>
>> > NERC Environmental Bioinformatics Centre
>>
>> >
>>
>> > Centre for Ecology and Hydrology
>>
>> > Maclean Bldg, Benson Lane
>>
>> > Crowmarsh Gifford
>>
>> > Wallingford, England
>>
>> > OX10 8BB
>>
>> >
>>
>> > http://nebc.nerc.ac.uk
>>
>> > +44 1491 69 2705
>>
>> >
>>
>>
>>
>> --
>>
>> Tim Booth <tbooth at ceh.ac.uk>
>>
>> NERC Environmental Bioinformatics Centre
>>
>>
>>
>> Centre for Ecology and Hydrology
>>
>> Maclean Bldg, Benson Lane
>>
>> Crowmarsh Gifford
>>
>> Wallingford, England
>>
>> OX10 8BB
>>
>>
>>
>> http://nebc.nerc.ac.uk
>>
>> +44 1491 69 2705
>>
>>
>>
>>
>>
>> Stephen P. Molnar, Ph.D. Life is a
>> fuzzy set
>>
>> (614)312-7528 (c)
>> Stochastic and
>> multivariate
>>
>> Skype: smolnar1
>>
>>
>>
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>>
>>
>
>
> --
> *********************************************
> Md Tauqeer Alam, Ph.D
> Division of Infectious Diseases
> Emory University School of Medicine
> 615 Michael Street, Atlanta, GA 30322, USA
> tauqeer9 at gmail.com
>
--
*********************************************
Md Tauqeer Alam, Ph.D
Division of Infectious Diseases
Emory University School of Medicine
615 Michael Street, Atlanta, GA 30322, USA
tauqeer9 at gmail.com
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