User: JunLVI

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JunLVI40
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Japan
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1 year, 3 months ago
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Posts by JunLVI

<prev • 47 results • page 2 of 5 • next >
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... # I tweaked the xml2-config into something like: #! /bin/sh prefix=/somewhere/Jun/Programme/libxml2-devel-2.9.1-2.1/usr exec_prefix=/somewhere/Jun/Programme/libxml2-devel-2.9.1-2.1/usr includedir=/somewhere/Jun/Programme/libxml2-devel-2.9.1-2.1/usr/include libdir=/somewhere/Jun/Programme/libxml2 ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... Hi Mike, thanks very much for your suggestion: which xml2-config ~/Programme/libxml2-devel-2.9.1-2.1/usr/bin/xml2-config # xml2-config is the one I installed xml2-config --cflags -I/usr/include/libxml2 xml2-config --libs -lxml2 -lz -lm -ldl # the xml2-config points at the system libraries. ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... @Marin Morgan, Thanks.  I tried to follow your suggestion. I guess that I managed to define xml-config. Somehow R automatically tried to get parser file from system libxml2 and performed the configuration using system libxml, despite the fact I xml-config was defined. I am trying to figure out how ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... (This is too long for one comment...) so I speculated that I could coerce R use my libxml2 by configuration (maybe I have done that with the “–enable” to “libpcre.so.1”), so I re configuration (re compile) R: ./configure --prefix=$HOME/Programme/R-3.3.1 --enable-R-shlib LDFLAGS="-L/$HOME/Programm ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... @Martin Morgan. Hi Martin, Thank you very much for your insightful suggestion.  > path = unclass(getLoadedDLLs()[["XML"]])$path > path [1] "/host/home/Jun/Programme/R-3.3.1/lib64/R/library/XML/libs/XML.so" > system2("ldd",args=path) linux-vdso.so.1 => (0x00007fff2a9e80 ...
written 2.7 years ago by JunLVI40
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Answer: A: Error with DESeq2 installation
... Hi, Alex. I had a similar issue when trying to install DiffBind.  Basically, "RcppArmadillo" requires a newer version of gcc.  I resolved the issue by installing a current version of gcc. You could just check the version of gcc you are using by  gcc --version   You should see something like: ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... The full output is just too long even after leaving out some parts, so I put it here as two replies. > biocLite("XML") BioC_mirror: http://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21). Installing package(s) ‘XML’ trying URL 'http://cran.rstudio.com/src/c ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... @ Hervé Pagès,  Thank you for your suggestion. Yes, I tried to re-install RCurl and XML, but the issue persisted.  Here is output of those two installation ( installations were done  without no overt errors, but some warnings during the process of installation) > biocLite("RCurl") Using ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... @Mike Smith, Thank for your kind suggestion. Yes, I tried to add the "http://rpm.pbone.net/index.php3/stat/4/idpl/23647961/dir/centos_5/com/libxml2-devel-2.9.1-2.1.noarch.rpm.html"   [myname@host ~]$ echo $CPATH /u32/myname/Programme/zlib-1.2.11/include/:/u32/myname/Programme/bzip2-1.0.6/includ ...
written 2.7 years ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... @Hervé Pagès, thanks very much for your suggestion.  I tried updating the Bioconductor to the current version. the "rtracklayer" was automatically updated as a dependency of DESeq2. Nonetheless, I installed rtracklayer with command, but the problem did persist, any further suggestion?   biocLite(" ...
written 2.7 years ago by JunLVI40

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