Re: [aroma.affymetrix] sfit fails

2011-05-15 Thread Henrik Bengtsson 
Hi.

First, have you tried to install the aroma framework using the following?

source(http://www.aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);

That should also install 'sfit' (from another server than R-forge).
Pay attention to the output when installing 'sfit' - if there's an
error, please let me know.

Second, R-forge does not provide binary builds of all packages,
specifically for 'sfit' (don't ask me why). This is probably why you
have problems installing directly from R-forge.

/Henrik

On Thu, May 12, 2011 at 8:06 PM, jasmine pfk...@gmail.com wrote:
 Hi,

 I encountered error in AllelicCrosstalkCalibration, where it says that
 sfit not found. I manually tried to install sfit but this is the error
 that I get. I am using R-2.12.2

 install.packages(sfit,
 repos=http://R-Forge.R-project.org,lib=~/R/library64;)
 trying URL 'http://R-Forge.R-project.org/src/contrib/
 sfit_0.1.9.tar.gz'
 Content type 'application/x-gzip' length 61695 bytes (60 Kb)
 opened URL
 ==
 downloaded 60 Kb

 * installing *source* package â ...
 ** libs
 ** arch -
 gcc -std=gnu99 -I/home/user/R/R-2.12.2/include  -I/usr/local/include
 -Wall -O3 -fpic  -g -O2 -c cfit.c -o cfit.o
 gcc -std=gnu99 -I/home/user/R/R-2.12.2/include  -I/usr/local/include
 -Wall -O3 -fpic  -g -O2 -c spa.c -o spa.o
 gcc -std=gnu99 -g -O2 -Wall -O3 cli.c cfit.o spa.o -o cfit -lm
 cli.c: In function â:
 cli.c:88: warning: â may be used uninitialized in this function
 cp cfit dummy.so
 mv cfit ../inst/bin/
 mv: cannot move `cfit' to `../inst/bin/': Not a directory
 make: *** [all] Error 1
 ERROR: compilation failed for package â
 * removing â

 The downloaded packages are in
        â
 Warning message:
 In install.packages(sfit, repos = http://R-Forge.R-project.org;,  :
  installation of package 'sfit' had non-zero exit status

 Thanks.

 --
 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.


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-- 
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.


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Re: [aroma.affymetrix] CustomCDF usage error

2011-05-15 Thread Henrik Bengtsson 
What is the name of your custom CDF, and what does print(cdf) report
after loading it with cdf - AffymetrixCdfFile$byName(...)?

/Henrik

On Wed, May 4, 2011 at 3:56 PM, Fong fongchunc...@gmail.com wrote:
 Hi all,

 I've created a customCDF following the procedure listed at:
 http://www.aroma-project.org/node/40

 The customCDF I made was based on the Brainarray group CDF (ense14 for
 Human Exon arrays to be exact).  I wanted to create a CDF which I
 could run FIRMA on since the customCDF provided by the BrainArray
 doesn't appear map the probeset (group ids) onto the appropriate gene
 (unit IDs) which is necessary to run FIRMA.  I create one that works
 in the flat2CDF() script provided by aroma.affymetrix and then when I
 used it on aroma affymetrix I got the following error:

 20110504 15:46:17|     Setting up ExonChipEffectFile...done
 20110504 15:46:17|    Retrieving chip-effect #19 of 20 (8_4N)...done
 20110504 15:46:17|    Retrieving chip-effect #20 of 20 (9_5T)...
 20110504 15:46:17|     Setting up ExonChipEffectFile...
 20110504 15:46:17|      Pathname: plmData/
 gardina_colon_cancer,ense14,QN,RMA,merged/HuEx-1_0-st-
 v2/9_5T,chipEffects.CEL
 20110504 15:46:17|     Setting up ExonChipEffectFile...done
 20110504 15:46:17|    Retrieving chip-effect #20 of 20 (9_5T)...done
 20110504 15:46:17|   Retrieving chip-effects from data set...done
 20110504 15:46:17|  Getting chip-effect set from data set...done
 20110504 15:46:17|  Updating ExonChipEffectSet...
 20110504 15:46:17|   Scanning for and applying sample annotation
 files...
 20110504 15:46:17|    Defining 0 files...

 20110504 15:46:17|    Defining 0 files...done
 20110504 15:46:17|    No sample annotation files found.
 20110504 15:46:17|   Scanning for and applying sample annotation
 files...done
 20110504 15:46:17|  Updating ExonChipEffectSet...done
 20110504 15:46:17|  Identifying non-fitted units in chip-effect
 file...
 20110504 15:46:17|   Pathname: plmData/
 gardina_colon_cancer,ense14,QN,RMA,merged/HuEx-1_0-st-
 v2/9_5T,chipEffects.CEL
 20110504 15:46:17|   Found indices cached on file
 20110504 15:46:17|   Reading data for these 442179 cells...
 Error in readCel(getPathname(this), indices = idxs, readIntensities =
 FALSE,  :
  Argument 'indices' is out of range [1,308580].
 Calls: fit ... findUnitsTodo - findUnitsTodo.ChipEffectFile -
 readCel
 20110504 15:46:17|   Reading data for these 442179 cells...done
 20110504 15:46:17|  Identifying non-fitted units in chip-effect
 file...done
 20110504 15:46:17| Identifying non-estimated units...done
 20110504 15:46:17|Fitting model of class ExonRmaPlm...done

 Has anyone run into this error before?  Any ideas on what I am doing
 wrong?

 Thanks,

 Fong

 --
 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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-- 
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 
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