Re: [gentoo-user] vm still grinding away at compiling webkitgtk-2.14.2

[J. Roeleveld]

On November 20, 2016 6:21:40 AM GMT+01:00, Alan McKinnon 
 wrote:
>On 20/11/2016 02:59, Harry Putnam wrote:
>> An emerge of webkitgtk-2.14.2 has been running for over 2hrs.  I
>> wonder if I am starving my vbox vm of gentoo with 3GB or ram.
>> 
>> Top's cpu usage is fluxuating between 45% and 99% during this compile
>> 
>> Portage pulling 99% by itself at times.
>> 
>> I thought 3GB was a bit high for a vm compared to what I've given
>debian
>> vms... can anyone give some guidance about how much ram to allow a
>> gentoo vm in Vbox?
>> 
>> I'm on a windows 10 host with 32 GB ram but running a number of vms.
>> 
>> 
>
>Depends on what you are compiling. webkitgtk is a brute, so is
>thunderbird, libreoffice and other usual culprits. Those sorts of build
>systems need as much ram as you can spare whereas the rest of the time
>vm itself needs as much as it needs to do whatever it is you want it to
>do.
>
>What hypervisor are you using, and can you use memory ballooning?

MS Windows desktop OSes are not the best platforms to run multiple VMs on.

Also, overcommitting CPUs has a bad influence on performance, especially if the 
host wants to use all cores as well.

I run VMs regularly and am not surprised at this.

I always use Linux as the host as the scheduler there works better for this 
kind of usage.

--
Joost
-- 
Sent from my Android device with K-9 Mail. Please excuse my brevity.

Re: [gentoo-user] Re: `sets' & sets.conf

[Alan McKinnon]

On 20/11/2016 02:43, Harry Putnam wrote:
> 
> [...]
> 
> Neil Bothwick  writes:
> 
>> You can create a set containing a list of packages. I do this for
>> dependencies of packages that are not from portage, so they don't get
>> depcleaned and don't end up in @world. Something like
> 
> [...]
> Thanks for the nifty examples... ... missing entirely in the pile of
> documenation at /usr/share/doc/portage-2.3.2/html/index.html
> (if you have USE=doc set)
> 
>> % cat /etc/portage/sets.conf
>> [kernels]
>> class = portage.sets.dbapi.OwnerSet
>> world-candidate = False
>> files = /usr/src
>>
>> then emerge -n @kernels
> 
> This one kind of sails right over my head... not seeing what is
> supposed to happen.
> 
> [...]
> 
> Alan McKinnon  writes:
> 
> [...]
> 
>> Think of it as sort of like a magic meta-package that you define - a set
>> gets merged as a unit and where you unmerge it, the sets is out of world
>> and depclean will take care of removing the members.
>>
>> Simple as that.  I'm not aware of anything in FEATURES related to sets,
>> you just use them out the box.
> 
> Gack, I was following along OK until the part about `out of the box'
> 
> Do you mean those toxic looking definitions or other stuff in the docs
> at /usr/share/doc/portage-2.3.2/html/index.html? ...
> 
> 


No, I mean:

install portage
vi /etc/portage/sets/mystuff
emerge @mystuff


-- 
Alan McKinnon
alan.mckin...@gmail.com

Re: [gentoo-user] vm still grinding away at compiling webkitgtk-2.14.2

[Alan McKinnon]

On 20/11/2016 02:59, Harry Putnam wrote:
> An emerge of webkitgtk-2.14.2 has been running for over 2hrs.  I
> wonder if I am starving my vbox vm of gentoo with 3GB or ram.
> 
> Top's cpu usage is fluxuating between 45% and 99% during this compile
> 
> Portage pulling 99% by itself at times.
> 
> I thought 3GB was a bit high for a vm compared to what I've given debian
> vms... can anyone give some guidance about how much ram to allow a
> gentoo vm in Vbox?
> 
> I'm on a windows 10 host with 32 GB ram but running a number of vms.
> 
> 

Depends on what you are compiling. webkitgtk is a brute, so is
thunderbird, libreoffice and other usual culprits. Those sorts of build
systems need as much ram as you can spare whereas the rest of the time
vm itself needs as much as it needs to do whatever it is you want it to do.

What hypervisor are you using, and can you use memory ballooning?

-- 
Alan McKinnon
alan.mckin...@gmail.com

Re: [gentoo-user] Re: elog default lifespan

[Alan McKinnon]

On 20/11/2016 02:21, Harry Putnam wrote:
> Mick  writes:
> 
>> On Saturday 19 Nov 2016 08:54:53 Harry Putnam wrote:
>>> After looking thru the portage man pages, the make.conf.example in
>>> /usr/share/portage/config, and the `Portage log wiki' it still is not
>>> clear to me how long elogs are kept if you use the `save' flag in
>>> make.conf or not.
>>>
>>> I did see something about '7 days' but it was not clear if that is the
>>> default and `save' over-rides it or what.  Or if there is another flag
>>> that controls there duration...
>>>
>>> Can anyone throw light on that?
>>
>> If you have logrotate then its configuration and associated cron jobs will 
>> take 
>> care of that.
> 
> What I want to know is if the elog program will do something on its
> own... I'm wanting to hang on to the logs a good while... I saw
> something in my readings about the elog system about 7 days... was not
> clear if that is a defalult or what.
> 
> So my fear was losing them even if I am logrotate at them in some
> capacity. So I'm asking about inside the elog program... what happens
> to the logs and when.
> 
> 


elog only appends to the log files. If you want rotation etc, use logrotate

-- 
Alan McKinnon
alan.mckin...@gmail.com

Re: [gentoo-user] libgcrypt-1.7.3 build fail

[Willie M]

On 11/10/2016 11:42 AM, Alon Bar-Lev wrote:
> Hi,
> Please open a bug.
> You probably updated gcc and should run revdep-rebuild or similar, see
> [1][2] for reference.
> Alon
> [1] https://bugs.gentoo.org/show_bug.cgi?id=561938
> [2] https://bugs.gentoo.org/show_bug.cgi?id=578302
> 
> On 10 November 2016 at 21:14, Willie M  > wrote:
> 
> Hey everyone,
> 
> I can not figure out why I cannot build libgcrypt-1.7.3. I had this same
> problem on my laptop but I can't remember what I did to fix the problem
> and have been searching on google for the last couple of days.
> 
> I have attached the build log. If anyone had any input please reply.
> 
> Thanks for any of your help,
> 
> --
> 
> Willie Matthews
> matthews.willi...@gmail.com 
> 
> 

I rebuilt glibc because they were talking about it in bug report
https://bugs.gentoo.org/show_bug.cgi?id=561938. So thanks a lot for your
help.

-- 

Willie Matthews
matthews.willi...@gmail.com



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Re: [gentoo-user] libgcrypt-1.7.3 build fail

[Willie M]

On 11/10/2016 11:42 AM, Alon Bar-Lev wrote:
> Hi,
> Please open a bug.
> You probably updated gcc and should run revdep-rebuild or similar, see
> [1][2] for reference.
> Alon
> [1] https://bugs.gentoo.org/show_bug.cgi?id=561938
> [2] https://bugs.gentoo.org/show_bug.cgi?id=578302
> 
> On 10 November 2016 at 21:14, Willie M  > wrote:
> 
> Hey everyone,
> 
> I can not figure out why I cannot build libgcrypt-1.7.3. I had this same
> problem on my laptop but I can't remember what I did to fix the problem
> and have been searching on google for the last couple of days.
> 
> I have attached the build log. If anyone had any input please reply.
> 
> Thanks for any of your help,
> 
> --
> 
> Willie Matthews
> matthews.willi...@gmail.com 
> 
> 

Thanks for your input. I finally got it working by building
sys-libs/glibc-2.22-r4. I have no idea why it worked or why I chose the
program to rebuild but we all get there somehow.

-- 

Willie Matthews
matthews.willi...@gmail.com



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[gentoo-user] vm still grinding away at compiling webkitgtk-2.14.2

[Harry Putnam]

An emerge of webkitgtk-2.14.2 has been running for over 2hrs.  I
wonder if I am starving my vbox vm of gentoo with 3GB or ram.

Top's cpu usage is fluxuating between 45% and 99% during this compile

Portage pulling 99% by itself at times.

I thought 3GB was a bit high for a vm compared to what I've given debian
vms... can anyone give some guidance about how much ram to allow a
gentoo vm in Vbox?

I'm on a windows 10 host with 32 GB ram but running a number of vms.

[gentoo-user] Re: `sets' & sets.conf

[Harry Putnam]

[...]

Neil Bothwick  writes:

> You can create a set containing a list of packages. I do this for
> dependencies of packages that are not from portage, so they don't get
> depcleaned and don't end up in @world. Something like

[...]
Thanks for the nifty examples... ... missing entirely in the pile of
documenation at /usr/share/doc/portage-2.3.2/html/index.html
(if you have USE=doc set)

> % cat /etc/portage/sets.conf
> [kernels]
> class = portage.sets.dbapi.OwnerSet
> world-candidate = False
> files = /usr/src
>
> then emerge -n @kernels

This one kind of sails right over my head... not seeing what is
supposed to happen.

[...]

Alan McKinnon  writes:

[...]

> Think of it as sort of like a magic meta-package that you define - a set
> gets merged as a unit and where you unmerge it, the sets is out of world
> and depclean will take care of removing the members.
>
> Simple as that.  I'm not aware of anything in FEATURES related to sets,
> you just use them out the box.

Gack, I was following along OK until the part about `out of the box'

Do you mean those toxic looking definitions or other stuff in the docs
at /usr/share/doc/portage-2.3.2/html/index.html? ...

[gentoo-user] Re: elog default lifespan

[Harry Putnam]

Mick  writes:

> On Saturday 19 Nov 2016 08:54:53 Harry Putnam wrote:
>> After looking thru the portage man pages, the make.conf.example in
>> /usr/share/portage/config, and the `Portage log wiki' it still is not
>> clear to me how long elogs are kept if you use the `save' flag in
>> make.conf or not.
>> 
>> I did see something about '7 days' but it was not clear if that is the
>> default and `save' over-rides it or what.  Or if there is another flag
>> that controls there duration...
>> 
>> Can anyone throw light on that?
>
> If you have logrotate then its configuration and associated cron jobs will 
> take 
> care of that.

What I want to know is if the elog program will do something on its
own... I'm wanting to hang on to the logs a good while... I saw
something in my readings about the elog system about 7 days... was not
clear if that is a defalult or what.

So my fear was losing them even if I am logrotate at them in some
capacity. So I'm asking about inside the elog program... what happens
to the logs and when.

Re: [gentoo-user] sans-dbus was: gnome intrusion?

[Rich Freeman]

On Sat, Nov 19, 2016 at 4:59 PM, Tom H  wrote:
> On Wed, Nov 16, 2016 at 7:47 AM, Miroslav Rovis
>  wrote:
>>
>> Ah, I almost forgot. Gentoo is as default (OpenRC) without dbus! Have a
>> look:
>>
>> https://wiki.gentoo.org/wiki/Comparison_of_init_systems
>>
>> There is no D-Bus under "Main dependencies" for OpenRC (I really like
>> OpenRC...)
>
> There's no reason that the fact that OpenRC doesn't depend on dbus
> should imply that something higher up the stack cannot depend on dbus!
>

I'd also comment that utilizing dbus and spawning random processes
that you don't understand are orthogonal issues.  Dbus is just an IPC
mechanism.

-- 
Rich

Re: [gentoo-user] sans-dbus was: gnome intrusion?

[Tom H]

On Wed, Nov 16, 2016 at 7:47 AM, Miroslav Rovis
 wrote:
>
> Ah, I almost forgot. Gentoo is as default (OpenRC) without dbus! Have a
> look:
>
> https://wiki.gentoo.org/wiki/Comparison_of_init_systems
>
> There is no D-Bus under "Main dependencies" for OpenRC (I really like
> OpenRC...)

There's no reason that the fact that OpenRC doesn't depend on dbus
should imply that something higher up the stack cannot depend on dbus!

Re: [gentoo-user] disabling IPv6 autoconfig for all interfaces

[Alarig Le Lay]

On Sat Nov 19 22:33:33 2016, J. Roeleveld wrote:
> doesn't work, I still get these:
> inet6 fe80::2e0:81ff:fecc:6ec6  prefixlen 64  scopeid 0x20
> 
> The problem with these (the mac-based ones) is that with multiple VLANs, they 
> all insist on using the same IP as they are all on the same physical device.

It’s a link-local IPv6, it’s normal to have at least one on each
interface. And you can have the same fe80 on several interfaces.

-- 
alarig


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Re: [gentoo-user] disabling IPv6 autoconfig for all interfaces

[J. Roeleveld]

On Saturday, November 19, 2016 09:13:14 PM Alarig Le Lay wrote:
> On Sat Nov 19 20:09:24 2016, J. Roeleveld wrote:
> > Hi all,
> > 
> > A related question: How do I prevent IPv6 addresses other than the ones I
> > DO configure?
> > 
> > Many thanks,
> > 
> > Joost
> 
> Hi,
> 
> You can do this with sysctl by setting the option
> net.ipv6.conf.$if.accept_ra to 0.

doesn't work, I still get these:
inet6 fe80::2e0:81ff:fecc:6ec6  prefixlen 64  scopeid 0x20

The problem with these (the mac-based ones) is that with multiple VLANs, they 
all insist on using the same IP as they are all on the same physical device.

--
Joost

Re: [gentoo-user] `sets' & sets.conf

[Alan McKinnon]

On 19/11/2016 18:04, Harry Putnam wrote:
> Can anyone post, in laymans, terms how to use sets.conf.  Or thru
> FEATURES if thats how its done, I've read the posrtage manpage that
> covers it and this URL:
> 
> https://dev.gentoo.org/~zmedico/portage/doc/ch02s02.html#config-set-syntax-single
> 
> Finally reinstalled portage with USE="doc" to get the html set
> referred to in portage manual as the definitive place to learn about sets
> 
> But honestly I left those without a stinking clue how to actually use sets
> for things like avoiding specific packages being depcleaned.  I mean
> besides putting them in `world'
> 
> There seems to be a durth of what actually to put into make.conf under
> FEATURES or whatever...
> 
> I want to protect certain pkgs from depclean how can I put a small
> list under `sets' management in make.conf or sets.conf or 
> 
> 


there are some rather old docs floating around that describe amazing
things you can do with sets, but I think those were flights of fantasy
and never got implemented. The main feature of sets is simply this:

list a bunch of packages in a text file in the right place, and the now
have a set named the same as the file name. You can emerge this set
using an "@" like:

emerge @harry_set

Effectively, the packages in @harry_set are effectively in world,
without actually being in the world file. The set instead is in
/var/lib/portage/world_sets.

Think of it as sort of like a magic meta-package that you define - a set
gets merged as a unit and where you unmerge it, the sets is out of world
and depclean will take care of removing the members.

Simple as that.  I'm not aware of anything in FEATURES related to sets,
you just use them out the box.


-- 
Alan McKinnon
alan.mckin...@gmail.com

Re: [gentoo-user] disabling IPv6 autoconfig for all interfaces

[Alarig Le Lay]

On Sat Nov 19 20:09:24 2016, J. Roeleveld wrote:
> Hi all,
> 
> A related question: How do I prevent IPv6 addresses other than the ones I DO 
> configure?
> 
> Many thanks,
> 
> Joost

Hi, 

You can do this with sysctl by setting the option
net.ipv6.conf.$if.accept_ra to 0.

-- 
alarig


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[gentoo-user] disabling IPv6 autoconfig for all interfaces

[J. Roeleveld]

Hi all,

For my VM server, I have several network interfaces and bridges configured.
I don't want every single interface and bridge to have an IPv6 address.

Only the one required for accessing the host will be sufficient.

What is the correct way to disable any form of autoconfiguration? Setting the 
config to "null":

eg:  config_eth0="null" 

only works for IPv4.

A related question: How do I prevent IPv6 addresses other than the ones I DO 
configure?

Many thanks,

Joost

Re: [gentoo-user] Doubt about R support in gentoo

[Zhu Sha Zang]

Yeah, thank you. ICU is a great pain in the ring!


Regards


On 11/19/2016 12:26 PM, c0a80...@gmail.com wrote:

On 11/19/16 12:50, Alec Ten Harmsel wrote:



El 19/11/2016 a las 07:47 a. m., Zhu Sha Zang escribió:


Hello everybody...


A single doubt here:


After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i
tried a package upgrade inside R and got that:


/> update.packages(checkBuilt=TRUE, ask=FALSE,
repos='http://cran.us.r-project.org')
trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz'
Content type 'application/x-gzip' length 1027358 bytes (1003 KB)
==
downloaded 1003 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  *unable to load shared object
'/usr/lib64/R/library/stringi/libs/stringi.so':**
**  libicui18n.so.57: cannot open shared object file: No such file or
directory*
/



I am not super familiar with R - can you try rebuilding R itself before
doing the CRAN package installs/upgrades? It looks like the path to ICU
is hard-coded somehow.



This kind of "bug" can I put inside bugs.gentoo.org or its a cran
package bug?

It is not the first time and i'm in dout about how to proceed.




If rebuildling R fixes this problem, you can file a bug so that
developers somehow trigger an R rebuild whenever ICU is updated.

Alec



Some R package update errors may be solved by creating a temporary 
folder, for example ~/R/tmp (placing it under ~/R has the advantage of 
sharing the same parent directory as the default per-user package 
library), and then passing the following environment variable to R: 
TMPDIR=$HOME/R/tmp. This allows certain configure scripts to be 
executed if your /tmp is mounted noexec.


As for the stringi error, my system doesn't have it in the system-wide 
library, either:


$ ls /usr/lib64/R/library/
KernSmooth  compilermgcvstats4
MASSdatasetsnlmesurvival
Matrix  foreign nnettcltk
basegrDevices   paralleltools
bootgraphicsrpart   translations
class   gridspatial utils
cluster lattice splines
codetools   methods stats

But:
$ ls ~/R/x86_64-pc-linux-gnu-library/3.2/stringi
AUTHORS LICENSE R   libs
CITATIONMetahelp
DESCRIPTION NAMESPACE   html
INDEX   NEWSinclude

Another possibility may be that your R has a useflag for icu (mine 
doesn't):


$ equery uses R
[ Legend : U - final flag setting for installation]
[: I - package is installed with flag ]
[ Colors : set, unset ]
 * Found these USE flags for dev-lang/R-3.2.2:
 U I
 ...
 + + doc : Add extra documentation (API, Javadoc, etc). It is
   recommended to enable per package instead of globally
 - - icu : Enable ICU (Internationalization Components for
   Unicode) support, using dev-libs/icu
 - - java: Add support for Java
 ...


Vitor

Re: [gentoo-user] `sets' & sets.conf

[Neil Bothwick]

On Sat, 19 Nov 2016 11:04:44 -0500, Harry Putnam wrote:

> Can anyone post, in laymans, terms how to use sets.conf.  Or thru
> FEATURES if thats how its done, I've read the posrtage manpage that
> covers it and this URL:
> 
> https://dev.gentoo.org/~zmedico/portage/doc/ch02s02.html#config-set-syntax-single
> 
> Finally reinstalled portage with USE="doc" to get the html set
> referred to in portage manual as the definitive place to learn about
> sets
> 
> But honestly I left those without a stinking clue how to actually use
> sets for things like avoiding specific packages being depcleaned.  I
> mean besides putting them in `world'
> 
> There seems to be a durth of what actually to put into make.conf under
> FEATURES or whatever...
> 
> I want to protect certain pkgs from depclean how can I put a small
> list under `sets' management in make.conf or sets.conf or 

You can create a set containing a list of packages. I do this for
dependencies of packages that are not from portage, so they don't get
depcleaned and don't end up in @world. Something like

% cat /etc/portage/sets/dependencies
### Needed by my python hacks
dev-python/beautifulsoup:4
dev-python/pyserial

### Needed by Prey
sys-apps/dmidecode

Then emerge -n @dependencies

sets.conf is used for other types of definition, I stop older kernels
being depcleaned with

% cat /etc/portage/sets.conf
[kernels]
class = portage.sets.dbapi.OwnerSet
world-candidate = False
files = /usr/src

then emerge -n @kernels


-- 
Neil Bothwick

MACINTOSH: Most Applications Crash; If Not, The Operating System Hangs


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Re: [gentoo-user] elog default lifespan

[Mick]

On Saturday 19 Nov 2016 08:54:53 Harry Putnam wrote:
> After looking thru the portage man pages, the make.conf.example in
> /usr/share/portage/config, and the `Portage log wiki' it still is not
> clear to me how long elogs are kept if you use the `save' flag in
> make.conf or not.
> 
> I did see something about '7 days' but it was not clear if that is the
> default and `save' over-rides it or what.  Or if there is another flag
> that controls there duration...
> 
> Can anyone throw light on that?

If you have logrotate then its configuration and associated cron jobs will take 
care of that.

-- 
Regards,
Mick

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Re: [gentoo-user] plain copy of root disk won't work

[Frank Steinmetzger]

On Fri, Nov 18, 2016 at 10:20:13PM +0300, Константин wrote:
> On Fri, Nov 18, 2016 at 04:30:28PM +0100, Raffaele BELARDI wrote:
> > I want to move the main disk contents (hda, PATA) to another, larger
> > disk (sda, SATA).
> >
> > hda contains 4 ext3 partitions (root, home, data, swap).
> > I created 4 ext3 partitions on sda and copied the data over from the
> > corresponding hda partitions using 'cp -ax'.
> 
> Didn't you do this from working system on hda? In this case there
> really could be troubles with special files etc. Imho live-cd better
> for this purpose.
> 
> At any case imho it's better to split this task
> 
> 0. Boot from live-cd.

If I can’t be bothered with live CDs, I bind-mount the root partition. I use
that frequently to do root-backups. That way you can get the files within
/dev which are required even before /dev is populated (null and zero, IIRC).
This will, of course, not prevent files from being changed during the rsync
run, because the system is still live and kicking. So I usually run it
several times to see what has changed in the meantime.

mkdir /mnt/bindroot
mount --bind / /mnt/bindroot
rsync -ahXAHi --delete /mnt/bindroot/ /path/to/new/partition/

Since this is a bindmount, no need for -x. Use -A and -X if you use acls and
xattrs, respectively. But you definitely want -H. For example git installs
all its commands as hardlinks to a single binary.

-- 
Gruß | Greetings | Qapla’
Please do not share anything from, with or about me with any social network.

Idealism grows with the distance to the problem.


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[gentoo-user] `sets' & sets.conf

[Harry Putnam]

Can anyone post, in laymans, terms how to use sets.conf.  Or thru
FEATURES if thats how its done, I've read the posrtage manpage that
covers it and this URL:

https://dev.gentoo.org/~zmedico/portage/doc/ch02s02.html#config-set-syntax-single

Finally reinstalled portage with USE="doc" to get the html set
referred to in portage manual as the definitive place to learn about sets

But honestly I left those without a stinking clue how to actually use sets
for things like avoiding specific packages being depcleaned.  I mean
besides putting them in `world'

There seems to be a durth of what actually to put into make.conf under
FEATURES or whatever...

I want to protect certain pkgs from depclean how can I put a small
list under `sets' management in make.conf or sets.conf or 

Re: [gentoo-user] Re: Doubt about R support in gentoo

[Zhu Sha Zang]

No, no overlay here. In fact I avoid overlay at any cost.

Thank you for a while!!


On 11/19/2016 12:36 PM, Michael Palimaka wrote:

On 20/11/16 01:47, Zhu Sha Zang wrote:

Hello everybody...


A single doubt here:


After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i tried
a package upgrade inside R and got that:


/> update.packages(checkBuilt=TRUE, ask=FALSE,
repos='http://cran.us.r-project.org')
trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz'
Content type 'application/x-gzip' length 1027358 bytes (1003 KB)
==
downloaded 1003 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   *unable to load shared object
'/usr/lib64/R/library/stringi/libs/stringi.so':**
**  libicui18n.so.57: cannot open shared object file: No such file or
directory*
Error : unable to load R code in package ‘knitr’
ERROR: lazy loading failed for package ‘knitr’
* removing ‘/usr/lib64/R/library/knitr’
* restoring previous ‘/usr/lib64/R/library/knitr’

The downloaded source packages are in
 ‘/tmp/RtmpKBphr0/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
   installation of package ‘knitr’ had non-zero exit status
/


This kind of "bug" can I put inside bugs.gentoo.org or its a cran
package bug?

It is not the first time and i'm in dout about how to proceed.


Thanks anyway.

Best regards!!

//


Due to the dev-libs/icu upgrade, the package that provides
/usr/lib64/R/library/stringi/libs/stringi.so needs to be rebuilt. I
assume you're using the R overlay, so that would be sci-CRAN/stringi.

It's possible for this rebuild to be achieved automatically in the
future, but it requires a minor modification to the stringi ebuild
(subslot operator to be added to dev-libs/icu dependency). As the R
overlay is automatically generated I'm not sure how to achieve this so
I've CCed Benda who I hope is the right person to look at this. :-)

[gentoo-user] Re: Doubt about R support in gentoo

[Michael Palimaka]

On 20/11/16 01:47, Zhu Sha Zang wrote:
> Hello everybody...
> 
> 
> A single doubt here:
> 
> 
> After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i tried
> a package upgrade inside R and got that:
> 
> 
> /> update.packages(checkBuilt=TRUE, ask=FALSE,
> repos='http://cran.us.r-project.org')
> trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz'
> Content type 'application/x-gzip' length 1027358 bytes (1003 KB)
> ==
> downloaded 1003 KB
> 
> * installing *source* package ‘knitr’ ...
> ** package ‘knitr’ successfully unpacked and MD5 sums checked
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   *unable to load shared object
> '/usr/lib64/R/library/stringi/libs/stringi.so':**
> **  libicui18n.so.57: cannot open shared object file: No such file or
> directory*
> Error : unable to load R code in package ‘knitr’
> ERROR: lazy loading failed for package ‘knitr’
> * removing ‘/usr/lib64/R/library/knitr’
> * restoring previous ‘/usr/lib64/R/library/knitr’
> 
> The downloaded source packages are in
> ‘/tmp/RtmpKBphr0/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages(update[instlib == l, "Package"], l, contriburl =
> contriburl,  :
>   installation of package ‘knitr’ had non-zero exit status
> /
> 
> 
> This kind of "bug" can I put inside bugs.gentoo.org or its a cran
> package bug?
> 
> It is not the first time and i'm in dout about how to proceed.
> 
> 
> Thanks anyway.
> 
> Best regards!!
> 
> //
> 

Due to the dev-libs/icu upgrade, the package that provides
/usr/lib64/R/library/stringi/libs/stringi.so needs to be rebuilt. I
assume you're using the R overlay, so that would be sci-CRAN/stringi.

It's possible for this rebuild to be achieved automatically in the
future, but it requires a minor modification to the stringi ebuild
(subslot operator to be added to dev-libs/icu dependency). As the R
overlay is automatically generated I'm not sure how to achieve this so
I've CCed Benda who I hope is the right person to look at this. :-)

Re: [gentoo-user] Doubt about R support in gentoo

[c0a800ff]

On 11/19/16 12:50, Alec Ten Harmsel wrote:



El 19/11/2016 a las 07:47 a. m., Zhu Sha Zang escribió:


Hello everybody...


A single doubt here:


After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i
tried a package upgrade inside R and got that:


/> update.packages(checkBuilt=TRUE, ask=FALSE,
repos='http://cran.us.r-project.org')
trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz'
Content type 'application/x-gzip' length 1027358 bytes (1003 KB)
==
downloaded 1003 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  *unable to load shared object
'/usr/lib64/R/library/stringi/libs/stringi.so':**
**  libicui18n.so.57: cannot open shared object file: No such file or
directory*
/



I am not super familiar with R - can you try rebuilding R itself before
doing the CRAN package installs/upgrades? It looks like the path to ICU
is hard-coded somehow.



This kind of "bug" can I put inside bugs.gentoo.org or its a cran
package bug?

It is not the first time and i'm in dout about how to proceed.




If rebuildling R fixes this problem, you can file a bug so that
developers somehow trigger an R rebuild whenever ICU is updated.

Alec



Some R package update errors may be solved by creating a temporary 
folder, for example ~/R/tmp (placing it under ~/R has the advantage of 
sharing the same parent directory as the default per-user package 
library), and then passing the following environment variable to R: 
TMPDIR=$HOME/R/tmp. This allows certain configure scripts to be executed 
if your /tmp is mounted noexec.


As for the stringi error, my system doesn't have it in the system-wide 
library, either:


$ ls /usr/lib64/R/library/
KernSmooth  compilermgcvstats4
MASSdatasetsnlmesurvival
Matrix  foreign nnettcltk
basegrDevices   paralleltools
bootgraphicsrpart   translations
class   gridspatial utils
cluster lattice splines
codetools   methods stats

But:
$ ls ~/R/x86_64-pc-linux-gnu-library/3.2/stringi
AUTHORS LICENSE R   libs
CITATIONMetahelp
DESCRIPTION NAMESPACE   html
INDEX   NEWSinclude

Another possibility may be that your R has a useflag for icu (mine doesn't):

$ equery uses R
[ Legend : U - final flag setting for installation]
[: I - package is installed with flag ]
[ Colors : set, unset ]
 * Found these USE flags for dev-lang/R-3.2.2:
 U I
 ...
 + + doc : Add extra documentation (API, Javadoc, etc). It is
   recommended to enable per package instead of globally
 - - icu : Enable ICU (Internationalization Components for
   Unicode) support, using dev-libs/icu
 - - java: Add support for Java
 ...


Vitor

Re: [gentoo-user] Doubt about R support in gentoo

[Alec Ten Harmsel]

El 19/11/2016 a las 07:47 a. m., Zhu Sha Zang escribió:


Hello everybody...


A single doubt here:


After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i 
tried a package upgrade inside R and got that:



/> update.packages(checkBuilt=TRUE, ask=FALSE, 
repos='http://cran.us.r-project.org')

trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz'
Content type 'application/x-gzip' length 1027358 bytes (1003 KB)
==
downloaded 1003 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
*unable to load shared object 
'/usr/lib64/R/library/stringi/libs/stringi.so':**
**  libicui18n.so.57: cannot open shared object file: No such file or 
directory*

/



I am not super familiar with R - can you try rebuilding R itself before 
doing the CRAN package installs/upgrades? It looks like the path to ICU 
is hard-coded somehow.




This kind of "bug" can I put inside bugs.gentoo.org or its a cran 
package bug?


It is not the first time and i'm in dout about how to proceed.




If rebuildling R fixes this problem, you can file a bug so that 
developers somehow trigger an R rebuild whenever ICU is updated.


Alec

[gentoo-user] Doubt about R support in gentoo

[Zhu Sha Zang]

Hello everybody...


A single doubt here:


After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i tried 
a package upgrade inside R and got that:



/> update.packages(checkBuilt=TRUE, ask=FALSE, 
repos='http://cran.us.r-project.org')

trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz'
Content type 'application/x-gzip' length 1027358 bytes (1003 KB)
==
downloaded 1003 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
*unable to load shared object 
'/usr/lib64/R/library/stringi/libs/stringi.so':**
**  libicui18n.so.57: cannot open shared object file: No such file or 
directory*

Error : unable to load R code in package ‘knitr’
ERROR: lazy loading failed for package ‘knitr’
* removing ‘/usr/lib64/R/library/knitr’
* restoring previous ‘/usr/lib64/R/library/knitr’

The downloaded source packages are in
‘/tmp/RtmpKBphr0/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = 
contriburl,  :

  installation of package ‘knitr’ had non-zero exit status
/


This kind of "bug" can I put inside bugs.gentoo.org or its a cran 
package bug?


It is not the first time and i'm in dout about how to proceed.


Thanks anyway.

Best regards!!

//

[gentoo-user] elog default lifespan

[Harry Putnam]

After looking thru the portage man pages, the make.conf.example in
/usr/share/portage/config, and the `Portage log wiki' it still is not
clear to me how long elogs are kept if you use the `save' flag in
make.conf or not.

I did see something about '7 days' but it was not clear if that is the
default and `save' over-rides it or what.  Or if there is another flag
that controls there duration...

Can anyone throw light on that?

Re: [gentoo-user] Firefox 49.0 & Youtube....Video: Yes - Audio: No...

[Miroslav Rovis]

On 161119-10:22+0100, Miroslav Rovis wrote:
> On 161119-00:33-0800, Daniel Campbell wrote:
...
> > > And there is a question/query/my-asking-for-advice further below.
...
> > >>> If jackd is to do with alsa, then it could be the following.
> > >>>
> > >>> Mozilla went pulse all the way:
> > >>>  Require PulseAudio on Linux
> > >>> https://bugzilla.mozilla.org/show_bug.cgi?id=1247056
> > >>> See also:
> > >>> Firefox nightly requires Pulse Audio
> > >>> http://forums.debian.net/viewtopic.php?f=20=130028
> > >>>
> >  Hmmm...
> > 
> >  Is there any fix for that?
> > >>> Not familiar with jackd. But as far as alsa (which I stick to, like
> > >>> other discontented users), I don't have sound since months ago.  The
> > >>> only way to get it would be to compile alsa myself, I'm afraid. 
> > >>>
...
> > > In that thred on alsa-user archive that I linked to, I got this link:
> > > 
> > > [linuxaudio.org] html5 in ff through jack
> > > http://lists.linuxaudio.org/pipermail/linux-audio-user/2016-June/thread.html#105188
...
> So it's only this, probably (and I had given links that, indirectly,
> mislead another Gentoo user...):
( No, it's not only this: )
> > Generally if you run into this problem, it's one of two things:
I've looked all options of my alsamixer, and it doesn't appear to me
that is's muted. I can play anything with MPlayer, and I can play an
HTML video by giving the url to Vlc...
> > 1. `alsamixer` hasn't been used to unmute the levels. After configuring
> > it, be sure to run 'alsactl store' as root and make sure the 'alsasound'
> > service is in the default run-level (`rc-update add alsasound default`
> > as root), or...
> > 2. Try adding these to your user's ~/.asoundrc file:

Also:
> > defaults.ctl.card x;
> > defaults.pcm.card x;
I every do often change my default card... I have only these two lines
(if I grep out all that is commented out) in my:
$ cat ~/.asoundrc | grep -v '^#'  

pcm.!default { type hw card 1 }
ctl.!default { type hw card 1 }

and sometimes I need to set it to 0, sometimes to 1 (depending of the
update of the system and where the old Hauppauge HVR3000's audio, or the
MBO's Intel HD Audio end up...

So this below is what I somehow practice since long:
> > Replace 'x' with the numeric index of your card (which you can view in
> > alsamixer using F6).
That does give the option to choose the card. But it's only one of the
two, the Hauppauge or the Intel HD...

Starting alsamixer and hitting F3 should be where to look for. And I
don't see anything the changing of which gives me audio to work in
Firefox...
> > If the order of your cards changes on boot, you'll
> > need to tell the module controlling your sound (snd_hda_intel is common)
> > to set its index in a file like /etc/modprobe.d/alsa-base.conf, with
> > lines like `options snd_hda_intel index=1` or something similar.
I have all built in the kernel. I do have audio, such as with MPlayer or
with Vlc, just I don't have audio in Firefox.

> > Others have done a far better job explaining this than me. Our own guide
> > on our wiki [0] and Arch's wiki [1] should be adequate to get you going
> > fairly quickly. Just Ctrl+F "default" to find what you need. Assuming
> > you don't have exotic hardware, this can be fixed in 15 minutes or less.
> > 
> > Hope this helps.
> > 
> > [0]: https://wiki.gentoo.org/wiki/ALSA#Configuration
> > [1]:
> > https://wiki.archlinux.org/index.php/Advanced_Linux_Sound_Architecture#Set_the_default_sound_card
It appears to be basically the same info as in your kind explanation...

But this is now getting way more than 15 minutes... I will try to find
more time, still, but not hours, for this issue...

> I don't think I even need to be back to report here if this just works
No, it doesn't. And the issue is not solved yet...

Regards!
-- 
Miroslav Rovis
Zagreb, Croatia
http://www.CroatiaFidelis.hr


signature.asc
Description: Digital signature

Re: [gentoo-user] split-elog setting

[Fernando Rodriguez]

On Sat, Nov 19, 2016 at 01:48:14AM -0500, Harry Putnam wrote:
> On gentoo `Portage log wiki' pages one is told:
> 
>  "In order to create per-category elog files, enable the split-elog
>  Portage feature."
> 
> (If you want to create `category-based' subdir.)
> 
> It never gets around to explaining how split-elog is enabled.
> 
> There is no example in /usr/share/portage/config/make.conf.example
> 
> Can anyone post an example of how and where this is done?
> 
> 

Add it to the FEATURES variable on /etc/portage/make.conf.
See the make.conf(5) man page for more info.

-- 
Fernando Rodriguez

Re: [gentoo-user] Firefox 49.0 & Youtube....Video: Yes - Audio: No...

[Miroslav Rovis]

On 161119-00:33-0800, Daniel Campbell wrote:
> On 11/18/2016 10:11 PM, Miroslav Rovis wrote:
> > Hi Meino!
> > 
> > I regret not having told you more... See below...
> > 
> > And there is a question/query/my-asking-for-advice further below.
> > 
> > On 161016-08:48+0200, meino.cra...@gmx.de wrote:
> >> Miroslav Rovis  [16-10-16 07:00]:
> >>> On 161015-20:27+0200, meino.cra...@gmx.de wrote:
>  Hi,
> 
>  this evening I updated GENTOO and a new firefox was installed.
>  This one seem completly to disable flash video finally...
>  since I got no video/audio at all.
> 
>  I disabled all flash-related addons of my firefox and
>  restarted  it.
> 
>  Now I got a video ... but without any audio.
>  (I am running jackd by the way).
>  I check with qjackctl whether there were any
>  ports which I missed to connect...nothing.
> >>>
> >>> If jackd is to do with alsa, then it could be the following.
> >>>
> >>> Mozilla went pulse all the way:
> >>>  Require PulseAudio on Linux
> >>> https://bugzilla.mozilla.org/show_bug.cgi?id=1247056
> >>> See also:
> >>> Firefox nightly requires Pulse Audio
> >>> http://forums.debian.net/viewtopic.php?f=20=130028
> >>>
>  Hmmm...
> 
>  Is there any fix for that?
> >>> Not familiar with jackd. But as far as alsa (which I stick to, like
> >>> other discontented users), I don't have sound since months ago.  The
> >>> only way to get it would be to compile alsa myself, I'm afraid. 
> >>>
> >>> Regards!
> >>> -- 
> >>> Miroslav Rovis
> >>> Zagreb, Croatia
> >>> http://www.CroatiaFidelis.hr
> >>
> >> Hi Miroslav,
> >>
> >> THANKS A LOT ! :)
> > You may not thank me, if you read my view, and even remotely agree:
> > http://www.mail-archive.com/alsa-user@lists.sourceforge.net/msg31926.html
> > ( and that is what I regret not having told you... I regret it because
> > you now may remain with that pulse spyware.. 
> > 
> > However, pls. note that in my first message to you I just said what the
> > reason was. I did not recommend pulse to you... )
> > 
> >> ...got it working...somehow...
> >>
> >> I installed pulseaudio and used pactl to set the default sink
> >> and source to the one soundcard (onboard), which is connected
> >> to my loudspeakers.
> >>
> >> Drawback: Setting the volume seems only to be tweakable via
> >> the volume slider of the HTML5 player in Firefox...and my alsa
> >> volume "app" of my taskbar doesn't work anymore.
> >>
> >> Hopefully the rest of my sound stuff still works
> >>
> > 
> > And now the question/query/my-asking-for-advice.
> > 
> > In that thred on alsa-user archive that I linked to, I got this link:
> > 
> > [linuxaudio.org] html5 in ff through jack
> > http://lists.linuxaudio.org/pipermail/linux-audio-user/2016-June/thread.html#105188
> > 
> > I'm gasping for free time to do various things, fixing audio in ff is
> > not of higest priority... Can not dedicate hours to this...
> > 
> > Anyone has a link for easy fixing of audio in Firefox the sans-pulse
> > way (and other poetterware excluded as well, of course)? With clear easy
> > steps, maybe?
> > 
> > Thanks in advance!

So it's only this, probably (and I had given links that, indirectly,
mislead another Gentoo user...):

> Generally if you run into this problem, it's one of two things:
> 
> 1. `alsamixer` hasn't been used to unmute the levels. After configuring
> it, be sure to run 'alsactl store' as root and make sure the 'alsasound'
> service is in the default run-level (`rc-update add alsasound default`
> as root), or...
> 2. Try adding these to your user's ~/.asoundrc file:
> 
> defaults.ctl.card x;
> defaults.pcm.card x;
> 
> Replace 'x' with the numeric index of your card (which you can view in
> alsamixer using F6). If the order of your cards changes on boot, you'll
> need to tell the module controlling your sound (snd_hda_intel is common)
> to set its index in a file like /etc/modprobe.d/alsa-base.conf, with
> lines like `options snd_hda_intel index=1` or something similar.
> 
> Others have done a far better job explaining this than me. Our own guide
> on our wiki [0] and Arch's wiki [1] should be adequate to get you going
> fairly quickly. Just Ctrl+F "default" to find what you need. Assuming
> you don't have exotic hardware, this can be fixed in 15 minutes or less.
> 
> Hope this helps.
> 
> [0]: https://wiki.gentoo.org/wiki/ALSA#Configuration
> [1]:
> https://wiki.archlinux.org/index.php/Advanced_Linux_Sound_Architecture#Set_the_default_sound_card
> -- 
> Daniel Campbell - Gentoo Developer
> OpenPGP Key: 0x1EA055D6 @ hkp://keys.gnupg.net
> fpr: AE03 9064 AE00 053C 270C  1DE4 6F7A 9091 1EA0 55D6

And here is a Gentoo developer who is helping us out:

https://dev.gentoo.org/~zlg/

Really thanks!

I don't think I even need to be back to report here if this just works
(will try it next), but I'll make sure I CC this to Meino...

Meino (for the Anglo folks, and for the only-English-as-foreign-language

Re: [gentoo-user] Firefox 49.0 & Youtube....Video: Yes - Audio: No...

[Daniel Campbell]

On 11/18/2016 10:11 PM, Miroslav Rovis wrote:
> Hi Meino!
> 
> I regret not having told you more... See below...
> 
> And there is a question/query/my-asking-for-advice further below.
> 
> On 161016-08:48+0200, meino.cra...@gmx.de wrote:
>> Miroslav Rovis  [16-10-16 07:00]:
>>> On 161015-20:27+0200, meino.cra...@gmx.de wrote:
 Hi,

 this evening I updated GENTOO and a new firefox was installed.
 This one seem completly to disable flash video finally...
 since I got no video/audio at all.

 I disabled all flash-related addons of my firefox and
 restarted  it.

 Now I got a video ... but without any audio.
 (I am running jackd by the way).
 I check with qjackctl whether there were any
 ports which I missed to connect...nothing.
>>>
>>> If jackd is to do with alsa, then it could be the following.
>>>
>>> Mozilla went pulse all the way:
>>>  Require PulseAudio on Linux
>>> https://bugzilla.mozilla.org/show_bug.cgi?id=1247056
>>> See also:
>>> Firefox nightly requires Pulse Audio
>>> http://forums.debian.net/viewtopic.php?f=20=130028
>>>
 Hmmm...

 Is there any fix for that?
>>> Not familiar with jackd. But as far as alsa (which I stick to, like
>>> other discontented users), I don't have sound since months ago.  The
>>> only way to get it would be to compile alsa myself, I'm afraid. 
>>>
>>> Regards!
>>> -- 
>>> Miroslav Rovis
>>> Zagreb, Croatia
>>> http://www.CroatiaFidelis.hr
>>
>> Hi Miroslav,
>>
>> THANKS A LOT ! :)
> You may not thank me, if you read my view, and even remotely agree:
> http://www.mail-archive.com/alsa-user@lists.sourceforge.net/msg31926.html
> ( and that is what I regret not having told you... I regret it because
> you now may remain with that pulse spyware.. 
> 
> However, pls. note that in my first message to you I just said what the
> reason was. I did not recommend pulse to you... )
> 
>> ...got it working...somehow...
>>
>> I installed pulseaudio and used pactl to set the default sink
>> and source to the one soundcard (onboard), which is connected
>> to my loudspeakers.
>>
>> Drawback: Setting the volume seems only to be tweakable via
>> the volume slider of the HTML5 player in Firefox...and my alsa
>> volume "app" of my taskbar doesn't work anymore.
>>
>> Hopefully the rest of my sound stuff still works
>>
> 
> And now the question/query/my-asking-for-advice.
> 
> In that thred on alsa-user archive that I linked to, I got this link:
> 
> [linuxaudio.org] html5 in ff through jack
> http://lists.linuxaudio.org/pipermail/linux-audio-user/2016-June/thread.html#105188
> 
> I'm gasping for free time to do various things, fixing audio in ff is
> not of higest priority... Can not dedicate hours to this...
> 
> Anyone has a link for easy fixing of audio in Firefox the sans-pulse
> way (and other poetterware excluded as well, of course)? With clear easy
> steps, maybe?
> 
> Thanks in advance!
> 
Generally if you run into this problem, it's one of two things:

1. `alsamixer` hasn't been used to unmute the levels. After configuring
it, be sure to run 'alsactl store' as root and make sure the 'alsasound'
service is in the default run-level (`rc-update add alsasound default`
as root), or...
2. Try adding these to your user's ~/.asoundrc file:

defaults.ctl.card x;
defaults.pcm.card x;

Replace 'x' with the numeric index of your card (which you can view in
alsamixer using F6). If the order of your cards changes on boot, you'll
need to tell the module controlling your sound (snd_hda_intel is common)
to set its index in a file like /etc/modprobe.d/alsa-base.conf, with
lines like `options snd_hda_intel index=1` or something similar.

Others have done a far better job explaining this than me. Our own guide
on our wiki [0] and Arch's wiki [1] should be adequate to get you going
fairly quickly. Just Ctrl+F "default" to find what you need. Assuming
you don't have exotic hardware, this can be fixed in 15 minutes or less.

Hope this helps.

[0]: https://wiki.gentoo.org/wiki/ALSA#Configuration
[1]:
https://wiki.archlinux.org/index.php/Advanced_Linux_Sound_Architecture#Set_the_default_sound_card
-- 
Daniel Campbell - Gentoo Developer
OpenPGP Key: 0x1EA055D6 @ hkp://keys.gnupg.net
fpr: AE03 9064 AE00 053C 270C  1DE4 6F7A 9091 1EA0 55D6



signature.asc
Description: OpenPGP digital signature