"Error in readRDS" while trying to install XML package
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@jasonharris-8540
Last seen 5.9 years ago
United States

I am trying to install rtracklayer, and got several errors.  I distilled the problem to the XML package (one of rtracklayer's dependencies).  Here is the console output when I try to do the installation:


> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
A newer version of Bioconductor is available after installing a new version of
  R, ?BiocUpgrade for help

> biocLite("XML")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'XML'

trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.98-1.3.tar.gz'
Content type 'application/x-gzip' length 1607725 bytes (1.5 Mb)

opened URL

==================================================

downloaded 1.5 Mb


* installing *source* package ‘XML’ ...

** package ‘XML’ 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/bin/xml2-config

USE_XML2 = yes

SED_EXTENDED_ARG: -E

Minor 7, Patch 6 for 2.7.6

Located parser file -I/usr/include/libxml2/parser.h

Checking for 1.8:  -I/usr/include/libxml2

Using libxml2.*

checking for gzopen in -lz... yes

checking for xmlParseFile in -lxml2... yes

checking for xmlHashSize in -lxml2... yes

Using built-in xmlHashSize

Checking DTD parsing (presence of externalSubset)...

checking for xmlHashSize in -lxml2... yes

Found xmlHashSize

checking for xmlOutputBufferCreateBuffer in -lxml2... yes

have xmlOutputBufferCreateBuffer()

checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes

checking libxml/xmlversion.h usability... yes

checking libxml/xmlversion.h presence... yes

checking for libxml/xmlversion.h... yes

Expat:  FALSE

Checking for return type of xmlHashScan element routine.

No return value for xmlHashScan

xmlNs has a context field

Checking for cetype_t enumeration

Using recent version of R with cetype_t enumeration type for encoding

checking for xmlsec1-config... no

nodegc default 

xml-debug default 

Version has XML_WITH_ZLIB

Version has xmlHasFeature()


****************************************

Configuration information:


Libxml settings


libxml include directory: -I/usr/include/libxml2

libxml library directory: -lxml2 -lz -lm -lz  -lxml2

libxml 2:                 -DLIBXML2=1


Compilation flags:         -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 

Link flags:               -lxml2 -lz -lm -lz  -lxml2


****************************************

configure: creating ./config.status

config.status: creating src/Makevars

config.status: creating R/supports.R

config.status: creating inst/scripts/RSXML.csh

config.status: creating inst/scripts/RSXML.bsh

** libs

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c DocParse.c -o DocParse.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c EventParse.c -o EventParse.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c ExpatParse.c -o ExpatParse.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c HTMLParse.c -o HTMLParse.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c NodeGC.c -o NodeGC.o

NodeGC.c: In function ‘clearNodeMemoryManagement’:

NodeGC.c:385: warning: comparison between pointer and integer

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c RSDTD.c -o RSDTD.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c RUtils.c -o RUtils.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c Rcatalog.c -o Rcatalog.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c Utils.c -o Utils.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c XMLEventParse.c -o XMLEventParse.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c XMLHashTree.c -o XMLHashTree.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c XMLTree.c -o XMLTree.o

XMLTree.c: In function ‘R_xmlSearchNs’:

XMLTree.c:1695: warning: comparison of distinct pointer types lacks a cast

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c fixNS.c -o fixNS.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c libxmlFeatures.c -o libxmlFeatures.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c schema.c -o schema.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c xmlsecurity.c -o xmlsecurity.o

gcc -std=gnu99 -I/nfs/common/apps/R-3.0.2/lib64/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2  -c xpath.c -o xpath.o

gcc -std=gnu99 -shared -L/usr/local/lib64 -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -lm -lz -lxml2 -L/nfs/common/apps/R-3.0.2/lib64/R/lib -lR

installing to /home/jharris/R/x86_64-unknown-linux-gnu-library/3.0/XML/libs

** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in readRDS(nsInfoFilePath) : error reading from connection
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/jharris/R/x86_64-unknown-linux-gnu-library/3.0/XML’

The downloaded source packages are in
    ‘/tmp/RtmpYVKLuj/downloaded_packages’

Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: installed directory not writable, cannot update packages 'boot', 'class',
  'cluster', 'codetools', 'colorspace', 'devtools', 'evaluate', 'foreign',
  'Formula', 'ggplot2', 'glmnet', 'gridExtra', 'gtools', 'Hmisc', 'httr',
  'jsonlite', 'KernSmooth', 'lattice', 'Matrix', 'matrixStats', 'mclust',
  'meta', 'mgcv', 'mime', 'mix', 'nlme', 'nnet', 'packrat', 'plotrix', 'R6',
  'Rcpp', 'RcppArmadillo', 'RCurl', 'rJava', 'RMySQL', 'roxygen2', 'rpart',
  'rstudioapi', 'R.utils', 'scales', 'spatial', 'stringr', 'survival', 'XML'
xml install • 1.7k views
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