

Hello, 

I am using R 2.10.0. The sessionInfo data is below at the end
of this message. I am using Ubuntu 10.04. 

I am trying to make a probe
package for a PM only Affy chip. I have altered the code for
AnnotationDbi's makeProbePackage.R to not look for MM probes (see code
pasted below). Then I installed the AnnotationDbi package from source, and
tried to prepare the package from my probe_tab file. 

Here is my code: 

>
filename outdir me species makeProbePackage("cb1190a520768f",
datafile=gzfile(filename,open="r"),outdir=outdir,maintainer=me,species=species,version="1.0",force=TRUE)Importing
the data.
Loading required package:
affy
***************************************************************************

Found different probe set names in 'CDF package' and 'probe package' for

4800 probes.
AFFX-BkGr-GC19_at PsedDRAFT_3064_at 
PsedDRAFT_0240_at
PsedDRAFT_3209_at 
PsedDRAFT_3109_at AFFX-BkGr-GC12_at 
PsedDRAFT_5914_at
PsedDRAFT_2727_at 
AFFX-BkGr-GC16_at AFFX-BkGr-GC19_at 
PsedDRAFT_1308_at
PsedDRAFT_4982_at 
AFFX-BkGr-GC17_at AFFX-BkGr-GC19_at 
PsedDRAFT_6011_at
AFFX-TrpnX-M_at 
PsedDRAFT_6222_at PsedDRAFT_0240_at 
AFFX-BkGr-GC16_at
PsedDRAFT_2460_at 
If you consider this mismatch insignificant, you may
want to rerun this
 function with 'comparewithcdf = FALSE'. Otherwise,
you'll need to
 figure out the reason for this!
Error in
.lgExtraParanoia(pt, cdfname) : Stopped
In addition: Warning messages:
1:
closing unused connection 5
(/home/bioinformatics/R/x86_64-pc-linux-gnu-library/2.10/AnnotationDbi/extdata/CB1190a520768F_probe_tab.gz)

2: closing unused connection 4
(/home/bioinformatics/R/x86_64-pc-linux-gnu-library/2.10/AnnotationDbi/extdata/CB1190a520768F_probe_tab.gz)

3: closing unused connection 3
(/home/bioinformatics/R/x86_64-pc-linux-gnu-library/2.10/AnnotationDbi/extdata/CB1190a520768F_probe_tab.gz)


---->Not sure why my CDF and probe list don't match - both were obtained
from Affymetrix.......So then I ran: 

> makeProbePackage("cb1190a520768f",
datafile=gzfile(filename,open="r"),outdir=outdir,maintainer=me,species=species,version="1.0",force=TRUE,
comparewithcdf=FALSE)
Importing the data.
Creating package in
/tmp/RtmpJxjLDw/cb1190a520768fcdfprobe 
Writing the data.
Checking the
package.
Error in makeProbePackage("cb1190a520768fcdf", datafile =
gzfile(filename, : 
 * checking whether package 'cb1190a520768fcdfprobe'
can be installed ... ERROR 

It looks like R wants to install the package,
but there is an unknown error. I though that maybe it was because i didn't
have administrative authority to write files, so i entered R by "sudo R",
but still the same thing. 

I would like to figure out what the error
pertains to.....Does any one have any pointers? 

Thanks, 

Ariel


locale:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 
 [3] LC_TIME=en_US.UTF-8
LC_COLLATE=en_US.UTF-8 
 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 
 [7]
LC_PAPER=en_US.UTF-8 LC_NAME=C 
 [9] LC_ADDRESS=C LC_TELEPHONE=C 
[11]
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 

attached base
packages:
[1] stats graphics grDevices utils datasets methods base 

other
attached packages:
[1] cb1190a520768fcdf_1.24.0 affy_1.24.2
AnnotationDbi_1.14.1 
[4] Biobase_2.6.1 

loaded via a namespace (and not
attached):
[1] affyio_1.14.0 DBI_0.2-5 preprocessCore_1.8.0
[4]
RSQLite_0.9-2 tools_2.10.1 

## On most chips, PM and MM probe are next to
each other on the chip, at same
 ## x coordinate and at adjacent y
coordinates. Then, "sizex" is always the same,
 ## namely the size of the
chip in x-direction. On some chips, there are few
 ## exceptions.
 ##tab =
table(mm1-pm1)
 tab = table(pm1)
 ## WHAT TO DO FOR THE ABOVE LINE?
 sizex
= as.numeric(names(tab))[ max(tab)==tab ]

 ## The probe indices according
to pt
 pm2 = pt$y * sizex + pt$x + 1
## Crossed out the mm2 function 
##
mm2 = (pt$y+1) * sizex + pt$x + 1
 psnm2 = pt[["Probe.Set.Name"]]

 ##
Check if the probe set names that are associated with each probe
 ## are
the same in both CDF and pt
 ## z1 = z2 = rep(NA, max(pm1, mm1, pm2, mm2))

## z1[pm1] = z1[mm1] = psnm1
 ## z2[pm2] = z2[mm2] = psnm2
## Remove mm1
and mm3 referals
z1 = z2 = rep(NA, max(pm1, pm2))
z1[pm1] = psnm1
z2[pm2] =
psnm2


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