Hi,
It looks like a problem with loading the shared object. I presume you
are using a Linux or
Mac system. Have you compiled the package from source or downloaded
the precompiled
version? If you've got the precompiled version then the C code is
compiled into a dll rather
than a shared object, and your system won't be able to open it.
Mike Smith
On 25 May 2007 at 15:39, Vincent Negre wrote:
> Hello,
> I can' t use the package snapCGH. Here is the error output. There is
a problem with snapCGH.so library.
>
> Somebody knows how to fix this problem.
>
> Your help will be greatly appreciated.
>
> Thank you.
>
> Vincent.
>
> PS: I'm using R version 2.5.0 on Mac OS X.
>
> > library(snapCGH)
> Le chargement a n?cessit? le package : tilingArray
> Le chargement a n?cessit? le package : affy
> Le chargement a n?cessit? le package : affyio
> Le chargement a n?cessit? le package : RColorBrewer
> Le chargement a n?cessit? le package : grid
> Le chargement a n?cessit? le package : strucchange
> Le chargement a n?cessit? le package : zoo
>
> Attachement du package : 'zoo'
>
>
> The following object(s) are masked from package:base :
>
> rapply
>
> Le chargement a n?cessit? le package : sandwich
> Le chargement a n?cessit? le package : vsn
> Le chargement a n?cessit? le package : genefilter
>
> Attachement du package : 'genefilter'
>
>
> The following object(s) are masked from package:MANOR :
>
> cv
>
> Le chargement a n?cessit? le package : geneplotter
> Le chargement a n?cessit? le package : annotate
> Le chargement a n?cessit? le package : lattice
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> Le chargement a n?cessit? le package : pixmap
>
> Attachement du package : 'tilingArray'
>
>
> The following object(s) are masked from package:DNAcopy :
>
> segment
>
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> impossible de charger la biblioth?que partag?e '/Library/Framewo
rks/R.framework/Versions/2.5/Resources/library/snapCGH/libs/ppc/snapCG
H.so':
> dlopen(/Library/Frameworks/R.framework/Versions/2.5/Resources/libr
ary/snapCGH/libs/ppc/snapCGH.so, 6): Library not loaded:
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libR.dylib
> Referenced from: /Library/Frameworks/R.framework/Versions/2.5/Reso
urces/library/snapCGH/libs/ppc/snapCGH.so
> Reason: image not found
> Erreur dans library(snapCGH) : .First.lib a ?chou? pour 'snapCGH'
> Error in dyn.unload(x) : la biblioth?que dynamique / partag?e '/Libr
ary/Frameworks/R.framework/Versions/2.5/Resources/library/snapCGH/libs
/snapCGH.so' n'a pas ?t? charg?e
>
>
> ---------------------------------
>
> [[alternative HTML version deleted]]
>
>
Hi friends,
I am having trouble parsing (it is not a download problem) some GEO
datasets using GEOquery. First I was using R 2.4.1 (GEOquery 1.8.0),
but
the error could be reproduced using R 2.5.0 (GEOquery 2.0.3).
In the example below, I could parse dataset GDS1080, but not GDS1082.
Is there anything I am doing wrong?
Thanks,
Saroj
--------------
> library(GEOquery)
> gds.1=getGEO("GDS1080")
trying URL
'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1080.soft.gz'
ftp data connection made, file length 694805 bytes
opened URL
downloaded 678Kb
File stored at:
...\Temp\RtmprrN1rb/GDS1080.soft.gz
parsing geodata
parsing subsets
ready to return
> gds.2=getGEO("GDS1082")
trying URL
'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1082.soft.gz'
ftp data connection made, file length 301168 bytes
opened URL
downloaded 294Kb
File stored at:
...\Temp\RtmprrN1rb/GDS1082.soft.gz
parsing geodata
parsing subsets
Error in strsplit(x, as.character(split), as.logical(extended),
as.logical(fixed), :
non-character argument in strsplit()
> sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets"
"methods"
[7] "base"
other attached packages:
GEOquery
"2.0.3"
----------------------
Saroj Mohapatra wrote:
> Hi friends,
>
> I am having trouble parsing (it is not a download problem) some GEO
> datasets using GEOquery. First I was using R 2.4.1 (GEOquery 1.8.0),
> but the error could be reproduced using R 2.5.0 (GEOquery 2.0.3).
>
> In the example below, I could parse dataset GDS1080, but not
GDS1082.
>
> Is there anything I am doing wrong?
Hi, Saroj. You are not doing anything wrong. GDS1082 is unusual in
that it contains no SUBSET tags. I was unaware that such GDS files
existed, so the code didn't deal with this situation. I have
corrected
the problem in the development version of GEOquery which should be
available in the next day or so. I will be changing the release
version
as well; look for a new version early next week. Thanks for the bug
report.
Sean
Sean:
Thanks for the response. I would use the new version of GEOquery when
it
becomes available.
Sincerely
Saroj
On Fri, May 25, 2007 10:52 pm, Sean Davis wrote:
> Saroj Mohapatra wrote:
>
>> Hi friends,
>>
>>
>> I am having trouble parsing (it is not a download problem) some GEO
>> datasets using GEOquery. First I was using R 2.4.1 (GEOquery
1.8.0), but
>> the error could be reproduced using R 2.5.0 (GEOquery 2.0.3).
>>
>> In the example below, I could parse dataset GDS1080, but not
GDS1082.
>>
>>
>> Is there anything I am doing wrong?
>>
> Hi, Saroj. You are not doing anything wrong. GDS1082 is unusual in
> that it contains no SUBSET tags. I was unaware that such GDS files
> existed, so the code didn't deal with this situation. I have
corrected
> the problem in the development version of GEOquery which should be
> available in the next day or so. I will be changing the release
version
> as well; look for a new version early next week. Thanks for the bug
> report.
>
> Sean
>
>
Sean:
Thanks for fixing the bug so promptly. I observed something new using
GEOquery 2.0.4. Parsing is fine, but it pauses with a "Browse[1]>". I
hit
enter and it moves on. I do not know why it halts, and I was planning
to
use the getGEO call as part of a script, not interactive. Is there
anyway
we could circumvent this?
Thanks,
Saroj
--------------------------------
> library("GEOquery")
> GDS1082=getGEO("GDS1082")
trying URL
'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1082.soft.gz'
using Synchronous WinInet calls
opened URL
downloaded 294Kb
File stored at:
C:\DOCUME~1\bookworm\LOCALS~1\Temp\Rtmppso3rb/GDS1082.soft.gz
parsing geodata
parsing subsets
Called from: parseGDSSubsets(txt)
Browse[1]>
ready to return
> sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets"
"methods"
[7] "base"
other attached packages:
GEOquery
"2.0.4"
-------------------------------------------
>> Hi, Saroj. You are not doing anything wrong. GDS1082 is unusual
in
>> that it contains no SUBSET tags. I was unaware that such GDS files
>> existed, so the code didn't deal with this situation. I have
corrected
>> the problem in the development version of GEOquery which should be
>> available in the next day or so. I will be changing the release
>> version as well; look for a new version early next week. Thanks
for the
>> bug report.
>>
>> Sean
>>
>>
>>
>
>
On Tuesday 29 May 2007 23:33, smohapat at vbi.vt.edu wrote:
> Sean:
>
> Thanks for fixing the bug so promptly. I observed something new
using
> GEOquery 2.0.4. Parsing is fine, but it pauses with a "Browse[1]>".
I hit
> enter and it moves on. I do not know why it halts, and I was
planning to
> use the getGEO call as part of a script, not interactive. Is there
anyway
> we could circumvent this?
Sorry, Saroj. This is fixed in version 2.0.5.
Sean
