[BioC] libxml2: incompatible library

Finak, Greg gfinak at scharp.org
Fri May 10 22:14:10 CEST 2013 

Frederico, 
flowStats doesn't depend on any specific version of the CRAN XML package. You can find that information in the DESCRIPTION file of all packages. If you check the Bioconductor logs (http://bioconductor.org/checkResults/devel/bioc-LATEST/) and (http://bioconductor.org/checkResults/2.12/bioc-LATEST/) you'll see it compiles and installs without issues on both the release and devel versions of Bioconductor. The problem you are having is caused by conflicting versions of the libxml C *library* (not the CRAN XML package) on your system. Likely, you have two versions of libxml installed, and one is being found by the compiler, while another is found by the linker at run time. Changing CRAN XML package versions is not going to help you. You need to pass appropriate compiler and linker flags when you build/install the CRAN XML package. Just taking a guess, having faced similar issues at times, I'd suggest downloading the XML package from CRAN and install it from the command line vi R CMD INSTALL, passing --configure-args=ARGS, with ARGS being your include and library path compiler flags pointing to a consistent version of libxml. You may end up having to also configure your LD_LIBRARY_PATH to ensure the location of the same version of the libxml library appears first. 
The maintainer of the XML package can be found here http://cran.r-project.org/web/packages/XML/index.html

Best,

Greg Finak
Staff Scientist
Vaccine and Infectious Disease Division
Fred Hutchinson Cancer Research Center
Seattle, WA
gfinak at fhcrc.org



On May 10, 2013, at 12:43 PM, Frederico Moraes Ferreira <ferreirafm at usp.br>
 wrote:

> Hi Greg,
> Thanks for your answer. Indeed, that's what the error message says.
> There isn't, however, any information about which XML package version flowStats depends on and if such dependency is direct or not. For this reason, I thought the flowStats mantainers would, possibly, provide such information. Thanks anyway.
> Has anybody have the e-mail of the XML package herd?
> Best,
> 
> -- 
> Dr. Frederico Moraes Ferreira
> Universy of Sao Paulo
> School of Medicine
> Heart Institute - Immunology Lab.
> Av. Dr. Enéas de Carvalho Aguiar, 44
> 05403-900     Sao Paulo - SP
> Brazil
> 
> 
> 
> 
> Em 10-05-2013 16:28, Finak, Greg escreveu:
>> This is an error installing the XML package, not the flowStats package.
>> Contact the maintainer of the XML package.
>> And, if you look at your error messages, you can see that you're likely having an issue with conflicting versions of libxml installed on your system.
>> 
>> 
>> Greg Finak
>> Staff Scientist
>> Vaccine and Infectious Disease Division
>> Fred Hutchinson Cancer Research Center
>> Seattle, WA
>> gfinak at fhcrc.org
>> 
>> 
>> 
>> On May 10, 2013, at 12:13 PM, "Fred [guest]" <guest at bioconductor.org>
>>  wrote:
>> 
>>> Hi list,
>>> I was try to install the flowStats package from Bioc and R stoped in checking phase before compilation. Here goes the log error.
>>> #######################################################
>>> * installing *source* package â?~XMLâ?T ...
>>> ** package â?~XMLâ?T successfully unpacked and MD5 sums checked
>>> checking for gcc... gcc
>>> checking for C compiler default output file name... a.out
>>> checking whether the C compiler works... yes
>>> checking whether we are cross compiling... no
>>> checking for suffix of executables...
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking how to run the C preprocessor... gcc -E
>>> checking for sed... /bin/sed
>>> checking for pkg-config... /usr/bin/pkg-config
>>> checking for xml2-config... /usr/local/programs/ccp4/ccp4-6.2.0/bin/xml2-config
>>> USE_XML2 = yes
>>> SED_EXTENDED_ARG: -E
>>> Minor 6, Patch 26 for 2.6.26
>>> Located parser file -I/usr/local/xtal/ccp4-6.2.0/include/libxml2/parser.h
>>> Checking for 1.8:  -I/usr/local/xtal/ccp4-6.2.0/include/libxml2
>>> Using libxml2.*
>>> checking for gzopen in -lz... yes
>>> checking for xmlParseFile in -lxml2... yes
>>> You are trying to use a version 2.* edition of libxml
>>> but an incompatible library. The header files and library seem to be
>>> mismatched. If you have specified LIBXML_INCDIR, make certain to also
>>> specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
>>> directories.
>>> ERROR: configuration failed for package â?~XMLâ?T
>>> * removing â?~/home/ferreirafm/R/x86_64-pc-linux-gnu-library/3.0/XMLâ?T
>>> ERROR: dependency â?~XMLâ?T is not available for package â?~flowWorkspaceâ?T
>>> * removing â?~/home/ferreirafm/R/x86_64-pc-linux-gnu-library/3.0/flowWorkspaceâ?T
>>> ERROR: dependency â?~flowWorkspaceâ?T is not available for package â?~flowStatsâ?T
>>> * removing â?~/home/ferreirafm/R/x86_64-pc-linux-gnu-library/3.0/flowStatsâ?T
>>> 
>>> The downloaded source packages are in
>>>        â?~/tmp/Rtmpur5nj8/downloaded_packagesâ?T
>>> Mensagens de aviso perdidas:
>>> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>  installation of package â?~XMLâ?T had non-zero exit status
>>> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>  installation of package â?~flowWorkspaceâ?T had non-zero exit status
>>> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>  installation of package â?~flowStatsâ?T had non-zero exit status
>>> #######################################################
>>> Please, let me know if you need additional information.
>>> Best,
>>> Fred
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> -- output of sessionInfo():
>>> 
>>>> sessionInfo()
>>> R version 3.0.0 (2013-04-03)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> 
>>> locale:
>>> [1] LC_CTYPE=pt_BR.UTF-8       LC_NUMERIC=C
>>> [3] LC_TIME=pt_BR.UTF-8        LC_COLLATE=pt_BR.UTF-8
>>> [5] LC_MONETARY=pt_BR.UTF-8    LC_MESSAGES=pt_BR.UTF-8
>>> [7] LC_PAPER=C                 LC_NAME=C
>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C
>>> 
>>> attached base packages:
>>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>> 
>>> other attached packages:
>>> [1] flowCore_1.26.0      rrcov_1.3-3          pcaPP_1.9-49
>>> [4] mvtnorm_0.9-9994     robustbase_0.9-7     Biobase_2.20.0
>>> [7] BiocGenerics_0.6.0   BiocInstaller_1.10.1
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] feature_1.2.8 graph_1.38.0  ks_1.8.12     MASS_7.3-26   stats4_3.0.0
>>> [6] tools_3.0.0
>>> 
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>> 
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>> 
> 
>

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