[BioC] RE : RE : rsamtools installation
Martin Morgan
mtmorgan at fhcrc.org
Fri Nov 18 14:41:44 CET 2011
On 11/18/2011 05:13 AM, Wolfgang RAFFELSBERGER wrote:
> Thank you Martin for taking your time to look into the problems indicated.
> Based on your help I was able to resolve both problems !!! In fact, an outdated version of zlib (as suspected not the copy in /usr/include/zlib.h ) was the problem for both errors I had reported (Rsamtools and RSQLite). So Martin did sense the problem really very well !
> I couldn't get the suggested ~/.R/Makevars going, but with Martin's hint on zlib.h I was already close enough.
>
> In line with the very helpful suggestions just one comment :
>
> When I was looking for the content of 'config.log' as cited during the installation (from inside R using biocLite() )
>> ... See `config.log' for more details. ...
> I couldn't find the config.log concerned. I checked the full R-installation path plus my home. I suppose that the config.log was in the path of the installation that finally was deleted as the installation failed ...
> Possibly there might be a way of preserving this information, or are there already existing parameters of the installation-command that I didn't realize ?
> The only way to preserve the log-file I see at this point is by installing as command line (also part of Martin's wize suggestions). Or are there smarter ways to do so ?
Installing by the command line is probably the easiest; R will typically
use a session-specific temporary directory (under tempdir()) where the
artifacts might be found. But once you end the R session, the directory
is cleaned up, so you lose the log...
Glad that you have straightened things out.
Martin
>
>
> Thank's again,
> Wolfgang
>
>
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> Wolfgang Raffelsberger, PhD
> IGBMC,
> 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
> Tel (+33) 388 65 3300 Fax (+33) 388 65 3201
> wolfgang.raffelsberger (at) igbmc.fr
>
> ________________________________________
> De : Martin Morgan [mtmorgan at fhcrc.org]
> Date d'envoi : mercredi 16 novembre 2011 06:37
> À : Wolfgang RAFFELSBERGER
> Cc : bioconductor at r-project.org
> Objet : Re: [BioC] RE : rsamtools installation
>
> On 11/14/2011 04:39 AM, Wolfgang RAFFELSBERGER wrote:
>> Dear List,
>> I have trouble too installing Rsamtools and RSQlite with R-2.14.0 on a RedHat system (installation of previous R& BioC versions had no problems on the same system).
>> In the case of RSQlite I'll try if there is a way of updating/grading our C compiler, but for Rsamtools I don't know what might be the problem (the file 'Rsamtools.so' actually exists in the folder 'Rsamtools').
>> Initially I ran into the problems using biocLite(), here I'lm reporting the specific messages when looking directly at Rsamtools and RSQlite.
>> Any hits are appreciated,
>
> Hi Wolfgang --
>
> For Rsamtools...
>
>>
>> Wolfgang
>>
>>
>>> source("http://www.bioconductor.org/biocLite.R")
>> BiocInstaller version 1.2.1, ?biocLite for help
>>>
>>> biocLite("Rsamtools")
>> BioC_mirror: 'http://www.bioconductor.org'
>> Using R version 2.14, BiocInstaller version 1.2.1.
>> Installing package(s) 'Rsamtools'
>> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtools_1.6.1.tar.gz'
>> Content type 'application/x-gzip' length 2088996 bytes (2.0 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.0 Mb
>>
>> * installing *source* package 'Rsamtools' ...
>> ** libs
> ...
>> gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/razf.c -o samtools/razf.o
>> samtools/razf.c:58:2: warning: #warning "zlib< 1.2.2.1; RAZF writing is disabled."
>
> the problem is that your zlib is too old :( from the top of my
> /usr/include/zlib.h (yours might be located elsewhere) I have
>
> /* zlib.h -- interface of the 'zlib' general purpose compression library
> version 1.2.3, July 18th, 2005
>
> I'm wondering whether your zlib really is that old, i.e., before 2005?
> I'm not sure why this would occur now, and not previously. Perhaps your
> R is finding a different zlib.h? You can create / edit a file
>
> ~/.R/Makevars
>
> to contain the line
>
> CFLAGS += "-v"
>
> and then from the command line after downloading Rsamtools.tar.gz
>
> tar xzf Rsamtools.tar.gz
> R CMD INSTALL Rsamtools
>
> and look for information like
>
> #include "..." search starts here:
> #include<...> search starts here:
> /home/mtmorgan/bin/R-2-14-branch/include
> /home/mtmorgan/R/x86_64-unknown-linux-gnu-library/2.14/Biostrings/include
> /home/mtmorgan/R/x86_64-unknown-linux-gnu-library/2.14/IRanges/include
> ./samtools
> ./samtools/bcftools
> ./tabix
> /usr/local/include
> /usr/lib64/gcc/x86_64-suse-linux/4.5/include
> /usr/lib64/gcc/x86_64-suse-linux/4.5/include-fixed
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/include
> /usr/include
> End of search list.
>
> and painstaking looking through the directories to find the first zlib.h.
>
> There have been changes in Rsamtools, including how it configures
> itself, so perhaps this is a symptom rather than cause.
>
>
>> ** testing if installed package can be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared object '/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/libs/Rsamtools.so':
>> /linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol: razf_write
>
> This is saying that razf_write is not found in Rsamtools.so; you can
> verify this, with a command like
>
> > R CMD nm Rsamtools/src/Rsamtools.so |grep razf_write
> 00000000000362b3 t _razf_write
> 0000000000036816 T razf_write
>
> on the .so created by R CMD INSTALL Rsamtools. The 'T' will be
> different, as described on the nm man page.
>
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing '/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools'
>>
>> The downloaded packages are in
>> '/tmp/RtmpN7ZA1O/downloaded_packaoges'
>> Updating HTML index of packages in '.Library'
>> Making packages.html ... done
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>> installation of package 'Rsamtools' had non-zero exit status
>>>
>>>
>>> ## following a recent related post on the list I tried what was suggested but this had no effect ...
>>>
>>> rm(biocLite)
>> Warning message:
>> In rm(biocLite) : object 'biocLite' not found
>>> rm(biocinstallRepos)
>> Warning message:
>> In rm(biocinstallRepos) : object 'biocinstallRepos' not found
>>>
>>>
>>>
>>> biocLite("RSQLite")
>> BioC_mirror: 'http://www.bioconductor.org'
>> Using R version 2.14, BiocInstaller version 1.2.1.
>> Installing package(s) 'RSQLite'
>> trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.10.0.tar.gz'
>> Content type 'application/x-gzip' length 1495533 bytes (1.4 Mb)
>> opened URL
>> ==================================================
>> downloaded 1.4 Mb
>>
>> * installing *source* package 'RSQLite' ...
>> ** package 'RSQLite' successfully unpacked and MD5 sums checked
>> checking for gcc...
>> gcc -std=gnu99
>> checking for C compiler default output file name...
>> configure: error: C compiler cannot create executables
>
> This one is strange, especially since you've just compiled Rsamtools! It
> might help to provide the last 20-30 lines of config.log
>
>> See `config.log' for more details.
>> configure: WARNING: Cache variable ac_cv_prog_ac_ct_CC contains a newline.
>> ERROR: configuration failed for package 'RSQLite'
>> * removing '/linux/biolo/R_star/R-2.14.0/lib64/R/library/RSQLite'
>>
>> The downloaded packages are in
>> '/tmp/RtmpU91PTB/downloaded_packages'
>> Updating HTML index of packages in '.Library'
>> Making packages.html ... done
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>> installation of package 'RSQLite' had non-zero exit status
>>>
>>>
>>> ## For completeness
>>>
>>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] BiocInstaller_1.2.1
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.14.0
>>
>>
>>
>> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>> Wolfgang Raffelsberger, PhD
>> IGBMC,
>> 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
>> Tel (+33) 388 65 3300 Fax (+33) 388 65 3201
>> wolfgang.raffelsberger (at) igbmc.fr
>>
>> ________________________________________
>> De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Xavier de Pedro [xavier.depedro at vhir.org]
>> Date d'envoi : lundi 14 novembre 2011 09:37
>> ? : Martin Morgan
>> Cc : kthom110 at uncc.edu; bioconductor at r-project.org
>> Objet : Re: [BioC] rsamtools installation
>>
>> Hi
>>
>> I was having a similar issue after upgrading to 2.14 and their
>> corresponding biocoonductor packages.
>>
>> And manually installing again bitops (and a few othes with a similar
>> issue for me), e.g.:
>>
>> biocLite("bitops")
>>
>> did the trick. For some reason, the older version didn'thave the
>> namespace that the new version of packages expects (for what I've noticed)
>>
>> Cheers
>>
>> Xavi
>>
>> On 11/11/11 20:00, Martin Morgan wrote:
>>> On 11/11/2011 09:55 AM, kevin [guest] wrote:
>>>>
>>>> hi,
>>>>
>>>> having difficulties installing Rsamtools, through biocLite:
>>>>
>>>> Warning: replacing previous import ?EUR?.__C__file?EUR(tm) when loading
>>>> ?EUR?Biostrings?EUR(tm)
>>>> Warning: replacing previous import ?EUR?.__C__connection?EUR(tm) when
>>>> loading ?EUR?Biostrings?EUR(tm)
>>>> Error : classes "file", "connection" are not exported by
>>>> 'namespace:Biostrings'
>>>> ERROR: lazy loading failed for package ?EUR?Rsamtools?EUR(tm)
>>>> * removing
>>>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools?EUR(tm)
>>>> * restoring previous
>>>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools?EUR(tm)
>>>>
>>>> The downloaded packages are in
>>>> ?EUR?/tmp/Rtmp6N3TVN/downloaded_packages?EUR(tm)
>>>> Warning message:
>>>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>>>> installation of package 'Rsamtools' had non-zero exit status
>>>>
>>>> and via R CMD INSTALL Rsamtools/
>>>>
>>>> Error : package 'bitops' does not have a name space
>>>> ERROR: lazy loading failed for package ?EUR?Rsamtools?EUR(tm)
>>>> * removing
>>>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools?EUR(tm)
>>>> * restoring previous
>>>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools
>>>>
>>>>
>>>> any help will be appreciated,
>>>> kevin
>>>>
>>>> -- output of sessionInfo():
>>>>
>>>> R version 2.12.1 (2010-12-16)
>>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>>
>>>> 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] Biostrings_2.22.0 IRanges_1.12.1
>>>
>>> Somehow you have managed to install Biostrings and IRanges for version
>>> 2.14 into your version 2.12 library; biocLite is trying to install the
>>> version of Rsamtools for 2.12 (presumably; there isn't enough info at
>>> the top).
>>>
>>> Your command line
>>>
>>>> and via R CMD INSTALL Rsamtools/
>>>>
>>>> Error : package 'bitops' does not have a name space
>>>
>>> implies that the R at the command line is version 2.14, i.e., you have
>>> multiple different versions of R installed on your system.
>>>
>>> I'd suggest starting again (with current R 2-14) and sticking with
>>> biocLite.
>>>
>>> Martin
>>>
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_2.12.1
>>>>
>>>>
>>>> --
>>>> Sent via the guest posting facility at bioconductor.org.
>>>>
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>>
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>
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>
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