Re: [aroma.affymetrix] Problems updating aroma.affymetrix
After updating to R-2.11.1, I no longer have this problem. Thanks.
Matt
On Thu, Sep 2, 2010 at 2:08 AM, Henrik Bengtsson wrote:
> Hi,
>
> if you are following Pierre's advice and still getting *that* error
> message my best guess is that you are getting an error while
> installing one of the packages that aroma.affymetrix depends on, which
> in turn probably will fail the installation of aroma.affymetrix
> itself. The reason why one of the required packages didn't install,
> may because your R version is far too old. So, update R, then retry
> again.
>
> More details: The installation code - hbInstall() - assumes that the
> installation went well and at the end tries to download and install
> patches. Since it did install well, you'll get that error on a too
> old version. I've updated that piece of the code not to try to patch
> if installation failed.
>
> Hope this helps
>
> Henrik
>
>
> On Wed, Sep 1, 2010 at 10:03 PM, Mark Robinson
> wrote:
> > Hi Matt.
> >
> > Another point to mention is that you should update your version of R ...
> 2.7.x is >2.5 years old, which is a long time in R. I'd recommend 2.11.x ..
> >
> > Cheers,
> > Mark
> >
> > On 2010-09-02, at 2:51 PM, Pierre Neuvial wrote:
> >
> >> [Forwarding this to the list so that others can read this thread]
> >>
> >> Pierre
> >>
> >> On Wed, Sep 1, 2010 at 12:57 PM, Matt wrote:
> >>> Hi Pierre,
> >>>
> >>> Thanks for the reply. I guess it's a problem with the source because
> what
> >>> you say is exactly what I did and I get the error message shown.
> >>>
> >>> Best,
> >>> Matt
> >>>
> >>> On Wed, Sep 1, 2010 at 3:20 PM, Pierre Neuvial <
> pie...@stat.berkeley.edu>
> >>> wrote:
>
> Hi Matt,
>
> You want to *update* the package, not *patch* it: the difference
> between updates and patches is explained at
> http://aroma-project.org/howtos/updateOrPatch.
>
> So, to update aroma.affymetrix, do:
>
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("aroma.affymetrix");
>
> as explained at http://aroma-project.org/install
>
> Hope this helps,
>
> Pierre.
>
> On Wed, Sep 1, 2010 at 10:08 AM, Matt wrote:
> > Hi there,
> >
> > I'd like to update my version of aroma.affymetrix, current version in
> > use 0.9.1, so that I can utilize the new CN processing method. I
> > followed the instructions on the site but I get the following error
> > message
> >
> > Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/
> > WeightsFile.R
> > Failed to source:
> > http://www.braju.com/R//patches/aroma.affymetrix/download.R
> > Error in stop(ex$message) :
> > Your version (0.9.1) of aroma.affymetrix is out of date. Please
> > update.
> > In addition: There were 11 warnings (use warnings() to see them)
> >> sessionInfo()
> > R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >
> >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] tools stats graphics grDevices datasets utils
> > methods
> > [8] base
> >
> > other attached packages:
> > [1] Biobase_2.0.1 aroma.affymetrix_0.9.1
> > aroma.apd_0.1.7
> > [4] R.huge_0.2.0 digest_0.4.2
> > aroma.light_1.16.1
> > [7] affxparser_1.12.2 R.rsp_0.3.6
> > R.cache_0.3.0
> > [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
> >
> >
> > How can I fix this?
> >
> > Thanks for any help.
> > Mattt
> >
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> > latest version of the package, 2) to report the output of
> sessionInfo() and
> > traceback(), and 3) to post a complete code example.
> >
> >
> > You received this message because you are subscribed to the Google
> > Groups "aroma.affymetrix" group with website
> http://www.aroma-project.org/.
> > To post to this group, send email to
> aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go to
> > http://www.aroma-project.org/forum/
> >
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of
> sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google
> Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to
> aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
> h
Re: [aroma.affymetrix] Problems updating aroma.affymetrix
Hi,
if you are following Pierre's advice and still getting *that* error
message my best guess is that you are getting an error while
installing one of the packages that aroma.affymetrix depends on, which
in turn probably will fail the installation of aroma.affymetrix
itself. The reason why one of the required packages didn't install,
may because your R version is far too old. So, update R, then retry
again.
More details: The installation code - hbInstall() - assumes that the
installation went well and at the end tries to download and install
patches. Since it did install well, you'll get that error on a too
old version. I've updated that piece of the code not to try to patch
if installation failed.
Hope this helps
Henrik
On Wed, Sep 1, 2010 at 10:03 PM, Mark Robinson wrote:
> Hi Matt.
>
> Another point to mention is that you should update your version of R ...
> 2.7.x is >2.5 years old, which is a long time in R. I'd recommend 2.11.x ..
>
> Cheers,
> Mark
>
> On 2010-09-02, at 2:51 PM, Pierre Neuvial wrote:
>
>> [Forwarding this to the list so that others can read this thread]
>>
>> Pierre
>>
>> On Wed, Sep 1, 2010 at 12:57 PM, Matt wrote:
>>> Hi Pierre,
>>>
>>> Thanks for the reply. I guess it's a problem with the source because what
>>> you say is exactly what I did and I get the error message shown.
>>>
>>> Best,
>>> Matt
>>>
>>> On Wed, Sep 1, 2010 at 3:20 PM, Pierre Neuvial
>>> wrote:
Hi Matt,
You want to *update* the package, not *patch* it: the difference
between updates and patches is explained at
http://aroma-project.org/howtos/updateOrPatch.
So, to update aroma.affymetrix, do:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
as explained at http://aroma-project.org/install
Hope this helps,
Pierre.
On Wed, Sep 1, 2010 at 10:08 AM, Matt wrote:
> Hi there,
>
> I'd like to update my version of aroma.affymetrix, current version in
> use 0.9.1, so that I can utilize the new CN processing method. I
> followed the instructions on the site but I get the following error
> message
>
> Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/
> WeightsFile.R
> Failed to source:
> http://www.braju.com/R//patches/aroma.affymetrix/download.R
> Error in stop(ex$message) :
> Your version (0.9.1) of aroma.affymetrix is out of date. Please
> update.
> In addition: There were 11 warnings (use warnings() to see them)
>> sessionInfo()
> R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices datasets utils
> methods
> [8] base
>
> other attached packages:
> [1] Biobase_2.0.1 aroma.affymetrix_0.9.1
> aroma.apd_0.1.7
> [4] R.huge_0.2.0 digest_0.4.2
> aroma.light_1.16.1
> [7] affxparser_1.12.2 R.rsp_0.3.6
> R.cache_0.3.0
> [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
>
>
> How can I fix this?
>
> Thanks for any help.
> Mattt
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo()
> and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google
> Groups "aroma.affymetrix" group with website
> http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to
http://www.aroma-project.org/forum/
>>>
>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> T
Re: [aroma.affymetrix] Problems updating aroma.affymetrix
Hi Matt.
Another point to mention is that you should update your version of R ... 2.7.x
is >2.5 years old, which is a long time in R. I'd recommend 2.11.x ..
Cheers,
Mark
On 2010-09-02, at 2:51 PM, Pierre Neuvial wrote:
> [Forwarding this to the list so that others can read this thread]
>
> Pierre
>
> On Wed, Sep 1, 2010 at 12:57 PM, Matt wrote:
>> Hi Pierre,
>>
>> Thanks for the reply. I guess it's a problem with the source because what
>> you say is exactly what I did and I get the error message shown.
>>
>> Best,
>> Matt
>>
>> On Wed, Sep 1, 2010 at 3:20 PM, Pierre Neuvial
>> wrote:
>>>
>>> Hi Matt,
>>>
>>> You want to *update* the package, not *patch* it: the difference
>>> between updates and patches is explained at
>>> http://aroma-project.org/howtos/updateOrPatch.
>>>
>>> So, to update aroma.affymetrix, do:
>>>
>>> source("http://aroma-project.org/hbLite.R";);
>>> hbInstall("aroma.affymetrix");
>>>
>>> as explained at http://aroma-project.org/install
>>>
>>> Hope this helps,
>>>
>>> Pierre.
>>>
>>> On Wed, Sep 1, 2010 at 10:08 AM, Matt wrote:
Hi there,
I'd like to update my version of aroma.affymetrix, current version in
use 0.9.1, so that I can utilize the new CN processing method. I
followed the instructions on the site but I get the following error
message
Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/
WeightsFile.R
Failed to source:
http://www.braju.com/R//patches/aroma.affymetrix/download.R
Error in stop(ex$message) :
Your version (0.9.1) of aroma.affymetrix is out of date. Please
update.
In addition: There were 11 warnings (use warnings() to see them)
> sessionInfo()
R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices datasets utils
methods
[8] base
other attached packages:
[1] Biobase_2.0.1 aroma.affymetrix_0.9.1
aroma.apd_0.1.7
[4] R.huge_0.2.0 digest_0.4.2
aroma.light_1.16.1
[7] affxparser_1.12.2 R.rsp_0.3.6
R.cache_0.3.0
[10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
How can I fix this?
Thanks for any help.
Mattt
--
When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google
Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to
http://www.aroma-project.org/forum/
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
--
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
--
__
The information in this email is confidential and intended solely for the
addressee.
You must not disclose, forward, print or use it without the permission of the
sender.
__
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a comple
Re: [aroma.affymetrix] Problems updating aroma.affymetrix
[Forwarding this to the list so that others can read this thread]
Pierre
On Wed, Sep 1, 2010 at 12:57 PM, Matt wrote:
> Hi Pierre,
>
> Thanks for the reply. I guess it's a problem with the source because what
> you say is exactly what I did and I get the error message shown.
>
> Best,
> Matt
>
> On Wed, Sep 1, 2010 at 3:20 PM, Pierre Neuvial
> wrote:
>>
>> Hi Matt,
>>
>> You want to *update* the package, not *patch* it: the difference
>> between updates and patches is explained at
>> http://aroma-project.org/howtos/updateOrPatch.
>>
>> So, to update aroma.affymetrix, do:
>>
>> source("http://aroma-project.org/hbLite.R";);
>> hbInstall("aroma.affymetrix");
>>
>> as explained at http://aroma-project.org/install
>>
>> Hope this helps,
>>
>> Pierre.
>>
>> On Wed, Sep 1, 2010 at 10:08 AM, Matt wrote:
>> > Hi there,
>> >
>> > I'd like to update my version of aroma.affymetrix, current version in
>> > use 0.9.1, so that I can utilize the new CN processing method. I
>> > followed the instructions on the site but I get the following error
>> > message
>> >
>> > Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/
>> > WeightsFile.R
>> > Failed to source:
>> > http://www.braju.com/R//patches/aroma.affymetrix/download.R
>> > Error in stop(ex$message) :
>> > Your version (0.9.1) of aroma.affymetrix is out of date. Please
>> > update.
>> > In addition: There were 11 warnings (use warnings() to see them)
>> >> sessionInfo()
>> > R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
>> > x86_64-unknown-linux-gnu
>> >
>> > locale:
>> >
>> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>> >
>> > attached base packages:
>> > [1] tools stats graphics grDevices datasets utils
>> > methods
>> > [8] base
>> >
>> > other attached packages:
>> > [1] Biobase_2.0.1 aroma.affymetrix_0.9.1
>> > aroma.apd_0.1.7
>> > [4] R.huge_0.2.0 digest_0.4.2
>> > aroma.light_1.16.1
>> > [7] affxparser_1.12.2 R.rsp_0.3.6
>> > R.cache_0.3.0
>> > [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
>> >
>> >
>> > How can I fix this?
>> >
>> > Thanks for any help.
>> > Mattt
>> >
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> > Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Problems updating aroma.affymetrix
Hi Matt,
You want to *update* the package, not *patch* it: the difference
between updates and patches is explained at
http://aroma-project.org/howtos/updateOrPatch.
So, to update aroma.affymetrix, do:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
as explained at http://aroma-project.org/install
Hope this helps,
Pierre.
On Wed, Sep 1, 2010 at 10:08 AM, Matt wrote:
> Hi there,
>
> I'd like to update my version of aroma.affymetrix, current version in
> use 0.9.1, so that I can utilize the new CN processing method. I
> followed the instructions on the site but I get the following error
> message
>
> Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/
> WeightsFile.R
> Failed to source: http://www.braju.com/R//patches/aroma.affymetrix/download.R
> Error in stop(ex$message) :
> Your version (0.9.1) of aroma.affymetrix is out of date. Please
> update.
> In addition: There were 11 warnings (use warnings() to see them)
>> sessionInfo()
> R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices datasets utils
> methods
> [8] base
>
> other attached packages:
> [1] Biobase_2.0.1 aroma.affymetrix_0.9.1
> aroma.apd_0.1.7
> [4] R.huge_0.2.0 digest_0.4.2
> aroma.light_1.16.1
> [7] affxparser_1.12.2 R.rsp_0.3.6
> R.cache_0.3.0
> [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
>
>
> How can I fix this?
>
> Thanks for any help.
> Mattt
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
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[aroma.affymetrix] Problems updating aroma.affymetrix
Hi there, I'd like to update my version of aroma.affymetrix, current version in use 0.9.1, so that I can utilize the new CN processing method. I followed the instructions on the site but I get the following error message Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/ WeightsFile.R Failed to source: http://www.braju.com/R//patches/aroma.affymetrix/download.R Error in stop(ex$message) : Your version (0.9.1) of aroma.affymetrix is out of date. Please update. In addition: There were 11 warnings (use warnings() to see them) > sessionInfo() R version 2.7.0 Under development (unstable) (2008-01-21 r44087) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices datasets utils methods [8] base other attached packages: [1] Biobase_2.0.1 aroma.affymetrix_0.9.1 aroma.apd_0.1.7 [4] R.huge_0.2.0 digest_0.4.2 aroma.light_1.16.1 [7] affxparser_1.12.2 R.rsp_0.3.6 R.cache_0.3.0 [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0 How can I fix this? Thanks for any help. Mattt -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
