Dear BioC users,
I encounter some troubles using affxparser, that causes R segfault. I
was originally using affyILM, which makes use of affxparser function
to
read cel files. As I got errors relating to affxparser, I then tested
affxparser with the following commands :
setwd("Datasets/ls133/HG-U133A_tag_Latin_Square")
library(affy)
cel<-list.celfiles()
library(affxparser)
readCelHeader(cel[1])
and get the following error :
*** caught segfault ***
address 0xfffffffc, cause 'memory not mapped'
Traceback:
1: .Call("R_affx_get_cel_file_header", filename, PACKAGE =
"affxparser")
2: readCelHeader(cel[1])
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Can you point me to some possible explanations for this R crash or
give
me instructions to solve the problem? I'm using the last release of R
and BioC on MacOSX. Never had troubles with previous releases.
Thanks,
Fabrice Berger
On Thu, Nov 17, 2011 at 6:26 AM, Fabrice Berger
<fabrice.berger at="" gmail.com=""> wrote:
> Dear BioC users,
>
> I encounter some troubles using affxparser, that causes R segfault.
I was
> originally using affyILM, which makes use of affxparser function to
read cel
> files. As I got errors relating to affxparser, I then tested
affxparser with
> the following commands :
>
> setwd("Datasets/ls133/HG-U133A_tag_Latin_Square")
> library(affy)
> cel<-list.celfiles()
> library(affxparser)
> readCelHeader(cel[1])
>
> and get the following error :
>
> ?*** caught segfault ***
> address 0xfffffffc, cause 'memory not mapped'
>
> Traceback:
> ?1: .Call("R_affx_get_cel_file_header", filename, PACKAGE =
"affxparser")
> ?2: readCelHeader(cel[1])
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> Can you point me to some possible explanations for this R crash or
give me
> instructions to solve the problem? I'm using the last release of R
and BioC
> on MacOSX. Never had troubles with previous releases.
Hi, Fabrice.
This has been reported on bioc-devel. The fix appears to be to
reinstall R using the most recent binary from CRAN and then reinstall
packages (perhaps not all need to be reinstalled, but it isn't clear
to me which are affected).
Sean
Hello Fabrice,
Thanks for the response.
It seems you are right; I did get affxparser installed using the
following:
> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("affxparser", type = "source")
And now Starr is working too.
Have a great day.
Noah
On Nov 17, 2011, at 10:26 AM, Fabrice Berger wrote:
> Hi Noah,
>
> I tested the Starr package and it seems to work for me. If
affxparser was installed on your system using the latest binary, I'm
not sure it will be installed from the sources using that command. Try
removing affxparser first, and then installing it from the sources.
>
> Fabrice
>
> On 17/11/11 16:55, Noah Dowell wrote:
>> Hello Fabrice,
>>
>> I was having the same problem using the Starr package(depends on
affxparser) and tried the following:
>>
>> To re-install affxparser alone using:
>>
>>> source("http://bioconductor.org/biocLite.R")
>> BiocInstaller version 1.2.1, ?biocLite for help
>>> update.packages("affxparser", repos=biocinstallRepos(), type=
"source")
>>
>> Is this the correct way to install from source (setting type =
"source")?
>>
>> In my case this did not prevent R from crashing.
>>
>> Thanks for any suggestions.
>>
>> Best,
>> Noah
>>
>>
>> On Nov 17, 2011, at 6:48 AM, Fabrice Berger wrote:
>>
>>> Dear BioC users,
>>>
>>> I could solve the problem.
>>>
>>> If some of you have the same troubles, I solved it by re-
installing affxparser from the sources instead of using the binary
package installed by default.
>>>
>>> Fabrice Berger
>>>
>
Dear BioC users,
I could solve the problem.
If some of you have the same troubles, I solved it by re-installing
affxparser from the sources instead of using the binary package
installed by default.
Fabrice Berger
------------------------------------
On 17/11/11 12:26, Fabrice Berger wrote:
> Dear BioC users,
>
> I encounter some troubles using affxparser, that causes R segfault.
I
> was originally using affyILM, which makes use of affxparser function
> to read cel files. As I got errors relating to affxparser, I then
> tested affxparser with the following commands :
>
> setwd("Datasets/ls133/HG-U133A_tag_Latin_Square")
> library(affy)
> cel<-list.celfiles()
> library(affxparser)
> readCelHeader(cel[1])
>
> and get the following error :
>
> *** caught segfault ***
> address 0xfffffffc, cause 'memory not mapped'
>
> Traceback:
> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE =
"affxparser")
> 2: readCelHeader(cel[1])
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> Can you point me to some possible explanations for this R crash or
> give me instructions to solve the problem? I'm using the last
release
> of R and BioC on MacOSX. Never had troubles with previous releases.
>
> Thanks,
>
> Fabrice Berger
>
Hello Fabrice,
I was having the same problem using the Starr package(depends on
affxparser) and tried the following:
To re-install affxparser alone using:
> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> update.packages("affxparser", repos=biocinstallRepos(), type=
"source")
Is this the correct way to install from source (setting type =
"source")?
In my case this did not prevent R from crashing.
Thanks for any suggestions.
Best,
Noah
On Nov 17, 2011, at 6:48 AM, Fabrice Berger wrote:
> Dear BioC users,
>
> I could solve the problem.
>
> If some of you have the same troubles, I solved it by re-installing
affxparser from the sources instead of using the binary package
installed by default.
>
> Fabrice Berger
>
> ------------------------------------
>
> On 17/11/11 12:26, Fabrice Berger wrote:
>> Dear BioC users,
>>
>> I encounter some troubles using affxparser, that causes R segfault.
I was originally using affyILM, which makes use of affxparser function
to read cel files. As I got errors relating to affxparser, I then
tested affxparser with the following commands :
>>
>> setwd("Datasets/ls133/HG-U133A_tag_Latin_Square")
>> library(affy)
>> cel<-list.celfiles()
>> library(affxparser)
>> readCelHeader(cel[1])
>>
>> and get the following error :
>>
>> *** caught segfault ***
>> address 0xfffffffc, cause 'memory not mapped'
>>
>> Traceback:
>> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE =
"affxparser")
>> 2: readCelHeader(cel[1])
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection:
>>
>> Can you point me to some possible explanations for this R crash or
give me instructions to solve the problem? I'm using the last release
of R and BioC on MacOSX. Never had troubles with previous releases.
>>
>> Thanks,
>>
>> Fabrice Berger
>>
>
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