Thank you very much for your tips.
It was sufficient to recompile all the installed  bioconductor packages to
solve the problem.

source("http://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
biocLite(pkgs)

Probably some updates of my ubuntu system broke the dependancies of some
packages.
Thank you again
Guido

2011/8/29 Harris A. Jaffee <hj@jhu.edu>

> On my system, gcc just runs whatever 'as' comes up first in my PATH.
> I wouldn't be surprised that this is typical, but it's possible that
> gcc would have its assembler configure in.
>
> If there an 'as' besides /usr/bin/as, this suggests a user environment
> foul-up rather than one by gcc or make.
>
> Anyway, I suggest working up from the bottom, by hand:
>
>        $ /usr/bin/as </dev/null && echo it worked
>
> If that works, try
>
>        $ as </dev/null && echo this worked also
>
> And just to make sure:
>
>        $ which as
>
> If all of these work, and the last one gives /usr/bin/as, then we are
> back to suspecting gcc itself or make.  Then the first thing to do is
> to see how gcc performs in a baby case like my command
>
>
>  $ strace -f -o debug_output_file gcc -o foo.o foo.c
>>
>
>
> Look for lines in the output containing "execve".  You will see what
> assembler is being exec'd and possibly the ENAMETOOLONG failure (see
> 'man 2 exec').
>
>
> On Aug 29, 2011, at 1:18 PM, Harris A. Jaffee wrote:
>
>  It sounds like it's the pathname to the assembler (as) which gcc wants to
>> execute, that is too long.  This could be a foul-up on the part of gcc or
>> make, and that will be a real nightmare to chase down.  Or perhaps he has
>> his own utility (maybe by accident) named "as" somewhere.  In this case,
>> the command
>>
>>        $ which as
>>
>> will be revealing.
>>
>> I would suspect that *any* compilation-with-assembly will fail, and this
>> just happens to be the first one that is being attempted.
>>
>> How about testing with a trivial C source file like this?
>>
>> foo.c:
>>
>> main()
>> {
>> printf("hello\n");
>> }
>>
>> The following command will need an assembler (and give some debugging):
>>
>> $ strace -f -o debug_output_file gcc -o foo.o foo.c
>>
>> On Aug 29, 2011, at 12:10 PM, Martin Morgan wrote:
>>
>>  On 08/29/2011 08:35 AM, Guido Leoni wrote:
>>>
>>>> Dear List I'm trying to update Biostrings package but every time with
>>>> the
>>>> same error message.
>>>>
>>>> * installing *source* package ‘Biostrings’ ...
>>>> ** libs
>>>> gcc -I/usr/share/R/include
>>>> -I"/home/guido/R/x86_64-pc-**linux-gnu-library/2.13/**IRanges/include"
>>>>   -fpic
>>>>  -std=gnu99 -O3 -pipe  -g -c BAB_class.c -o BAB_class.o
>>>> gcc: error trying to exec 'as': execvp: File name too long
>>>> make: *** [BAB_class.o] Error 2
>>>> ERROR: compilation failed for package ‘Biostrings’
>>>>
>>>
>>> Weird. Do other packages requiring source build work, e.g., Biobase? If
>>> not, it sounds like a system configuration issue. If so, try updating
>>> IRanges, then Biostrings?
>>>
>>> I'm not sure what else to suggest, perhaps downloading the Biostrings
>>> source (as tar.gz) and running from the command line
>>>
>>>  CFLAGS="-v" R CMD INSTALL --libs-only Biostrings_2.20.3.tar.gz
>>>
>>> and looking for a suspicious path name that might actually trigger the
>>> 'File name too long' message.
>>>
>>> Martin
>>>
>>>  * removing ‘/home/guido/R/x86_64-pc-**linux-gnu-library/2.13/**
>>>> Biostrings’
>>>> * restoring previous
>>>> ‘/home/guido/R/x86_64-pc-**linux-gnu-library/2.13/**Biostrings’
>>>> This is my sessionInfo()
>>>> R version 2.13.0 (2011-04-13)
>>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>>
>>>> locale:
>>>>  [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C
>>>>  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8
>>>>  [5] LC_MONETARY=C              LC_MESSAGES=it_IT.UTF-8
>>>>  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C
>>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tcltk_2.13.0 tools_2.13.0
>>>>
>>>>
>>>> Any idea?
>>>> Thank you very much
>>>> Guido
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
-- 
Guido Leoni
National Research Institute on Food and Nutrition
(I.N.R.A.N.)
via Ardeatina 546
00178 Rome
Italy

tel     + 39 06 51 49 41 (operator)
        + 39 06 51 49 4498 (direct)

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