Problems loading biomaRt and XML
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@jordi-altirriba-gutierrez-682
Last seen 3.5 years ago
Dear BioC users, I am trying to run biomaRt, but I am not able to do it. I install (in R under Windows OS) biomaRt through: Packages -> Install package(s) -> biomaRt Then I load it: >library(biomaRt) Loading required package: XML Error: package 'XML' could not be loaded Adem?s: Warning message: there is no package called 'XML' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) After this I install XML (without any problems) and I re-load biomaRt, but an error message appears in a new window (I am translating it, as the messages are in Spainsh): The entrance point of _htmlDefaultSAXHandler procedure can?t be found in the library of dynamic links libxml2.dll Moreover in the R window appears: Loading required package: XML Error in dyn.load(x, as.logical(local), as.logical(now)) : impossible to load the shared library 'C:/ARCHIV~1/R/R-23~1.1/library/XML/libs/XML.dll': LoadLibrary failure: The specified process was no found. Error: .onLoad failed in 'loadNamespace' for 'XML' Error: package 'XML' could not be loaded I have removed R and reinstalled it, and repeated all the process; nevertheless the errors are the same. I have tried to found a solution in Google and gmane, although I don?t have been able to found it. >sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" Many thanks in advance for your help! Yours faithfully, Jordi Altirriba PhD student Hospital Clinic, Barcelona, Spain
PROcess biomaRt PROcess biomaRt • 1.8k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.1 years ago
Hi Jordi, Jordi Altirriba Guti?rrez <altirriba at="" hotmail.com=""> writes: > After this I install XML (without any problems) and I re-load biomaRt, but > an error message appears in a new window (I am translating it, as the > messages are in Spainsh): > > The entrance point of _htmlDefaultSAXHandler procedure can.t be found in the > library of dynamic links libxml2.dll > > Moreover in the R window appears: > > Loading required package: XML > Error in dyn.load(x, as.logical(local), as.logical(now)) : > impossible to load the shared library > 'C:/ARCHIV~1/R/R-23~1.1/library/XML/libs/XML.dll': > LoadLibrary failure: The specified process was no found. > Error: .onLoad failed in 'loadNamespace' for 'XML' > Error: package 'XML' could not be loaded What version of the XML package did you download? Perhaps try one more time with biocLite: source("http://bioconductor.org/biocLite.R") biocLite("XML") Then try just: library("XML") I'm guessing that somehow you ended up with a bad/old version of the XML package, but am not sure. + seth
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@jordi-altirriba-gutierrez-682
Last seen 3.5 years ago
Dear Seth, Thanks for your answer. >What version of the XML package did you download? Perhaps try one >more time with biocLite: > source("http://bioconductor.org/biocLite.R") > biocLite("XML") > library("XML") > >I'm guessing that somehow you ended up with a bad/old version of the >XML package, but am not sure. The version of XML is 0.99-7. ----------------- I've tried to obtain it from CRAN, from the Madrid and the London mirror, but I am obtaining the same results: ... trying the URL 'http://cran.es.r-project.org/bin/windows/contrib/2.3/XML_0.99-7.zip' ... trying the URL 'http://www.sourcekeg.co.uk/cran/bin/windows/contrib/2.3/XML_0.99-7.zi p' ... package 'XML' successfully unpacked and MD5 sums checked (in both cases) >library (biomaRt) (or library (XML)) The same error described below. ---------------------------------- I have used BioCLite, as you suggested, which obtains XML from Omegahat, obtaining: >source("http://bioconductor.org/biocLite.R") >biocLite("XML") Running getBioC version 0.1.6 with R version 2.3.1 Running biocinstall version 1.8.4 with R version 2.3.1 Your version of R requires version 1.8 of Bioconductor. trying the URL 'http://bioconductor.org/packages/1.8/omegahat/bin/windows/contrib/2.3 /XML_0.99-7.zip' Content type 'application/zip' length 1323552 bytes URL opened downloaded 1292Kb package 'XML' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\BIO SANTANDER\Configuraci?n local\Temp\RtmpIZV3pb\downloaded_packages updating HTML package descriptions >library(XML) The same error described below. ------------------------------- Any other suggestion? Many thanks for your suggestions and time! Yours sincerely, Jordi Altirriba PhD student Hospital Clinic, Barcelona, Spain >Jordi Altirriba Guti?rrez <altirriba at="" hotmail.com=""> writes: >>After this I install XML (without any problems) and I re-load biomaRt, but >>an error message appears in a new window (I am translating it, as the >>messages are in Spainsh): >> >>The entrance point of _htmlDefaultSAXHandler procedure can.t be found in >>the library of dynamic links libxml2.dll >> >>Moreover in the R window appears: >> >>Loading required package: XML >>Error in dyn.load(x, as.logical(local), as.logical(now)) : >> impossible to load the shared library >>'C:/ARCHIV~1/R/R-23~1.1/library/XML/libs/XML.dll': >> LoadLibrary failure: The specified process was no found. >>Error: .onLoad failed in 'loadNamespace' for 'XML' >>Error: package 'XML' could not be loaded
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.1 years ago
Jordi Altirriba Guti?rrez <altirriba at="" hotmail.com=""> writes: > The version of XML is 0.99-7. > > ----------------- > > I've tried to obtain it from CRAN, from the Madrid and the London > mirror, but I am obtaining the same results: > ... > ---------------------------------- > > I have used BioCLite, as you suggested, which obtains XML from > Omegahat, obtaining: > > package 'XML' successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Documents and Settings\BIO SANTANDER\Configuraci?n > local\Temp\RtmpIZV3pb\downloaded_packages > updating HTML package descriptions >>library(XML) > > The same error described below. > > ------------------------------- > > Any other suggestion? I would examine your PATH (environment variable) and also search for all instances of the libxml2.dll DLL on your system. Another possibility is that you are picking up a different DLL than the one that comes with the XML package. The XML package does seem to be working for others on Windows... + seth
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