Re: [aroma.affymetrix] Problems updating aroma.affymetrix

2010-09-02 Thread Henrik Bengtsson
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 mrobin...@wehi.edu.au 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 matt.kowg...@gmail.com 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 matt.kowg...@gmail.com 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  Your version (0.9.1) of aroma.affymetrix is out of date.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
 --






Re: [aroma.affymetrix] Problems updating aroma.affymetrix

2010-09-02 Thread Matt
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 h...@stat.berkeley.eduwrote:

 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 mrobin...@wehi.edu.au
 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 matt.kowg...@gmail.com 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 matt.kowg...@gmail.com 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
 

[aroma.affymetrix] Problems updating aroma.affymetrix

2010-09-01 Thread Matt
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/