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Question: Error in CummeRbund installation
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gravatar for ivonyao
2.2 years ago by
ivonyao0
United States
ivonyao0 wrote:

Hi,

I am really new for this.   I have analyzed my RNA-Seq data using TopHat and cufflinks/cuffdiff. I would now like to visualize the results from cuffdiff using cummeRbund. I have the latest installation of R (3.2.1), but when I try to install cummeRbund by following the instructions on the Bioconductor website, I keep getting same error. I'm not sure what the problem is, unfortunately :( See copy/pasted text below).

Can anyone help? Thank you!

 

source("http://bioconductor.org/biocLite.R")
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  SpeedThe downloaded binary packages are in

    /var/folders/f_/7p8pfw9s5ps2yndz1yj3fsxc0000gn/T//RtmpkJkVzp/downloaded_packages
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1.
Installing package(s) ‘cummeRbund’
also installing the dependencies ‘lambda.r’, ‘futile.options’, ‘colorspace’, ‘futile.logger’, ‘snow’, ‘Formula’, ‘acepack’, ‘gridExtra’, ‘dichromat’, ‘munsell’, ‘labeling’, ‘stringi’, ‘magrittr’, ‘bitops’, ‘BiocParallel’, ‘Hmisc’, ‘VariantAnnotation’, ‘DBI’, ‘digest’, ‘gtable’, ‘scales’, ‘proto’, ‘stringr’, ‘Rcpp’, ‘GenomicRanges’, ‘XML’, ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’, ‘Biostrings’, ‘zlibbioc’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’, ‘RColorBrewer’, ‘biomaRt’, ‘AnnotationDbi’, ‘GenomicFeatures’, ‘BSgenome’, ‘biovizBase’, ‘latticeExtra’, ‘matrixStats’, ‘BiocGenerics’, ‘RSQLite’, ‘ggplot2’, ‘reshape2’, ‘fastcluster’, ‘rtracklayer’, ‘Gviz’, ‘plyr’, ‘Biobase’


  There are binary versions available but the source versions are later:
        binary   source needs_compilation
Hmisc   3.16-0   3.17-0              TRUE
XML   3.98-1.2 3.98-1.3              TRUE

The downloaded binary packages are in
    /var/folders/f_/7p8pfw9s5ps2yndz1yj3fsxc0000gn/T//RtmpkJkVzp/downloaded_packages

installing the source packages ‘Hmisc’, ‘XML’

gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Hmisc.c -o Hmisc.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2  -c cidxcn.f -o cidxcn.o
make: gfortran-4.2: No such file or directory
make: *** [cidxcn.o] Error 1
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Hmisc’
* 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... /usr/bin/sed
checking for pkg-config... no
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 7, Patch 8 for 2.7.8
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  -lxml2
libxml 2:                 -DLIBXML2=1

Compilation flags:         -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 ->>>>>>> 
Link flags:               -lxml2 -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.......

......................


XMLTree.c: In function ‘R_xmlSearchNs’:
XMLTree.c:1695: warning: comparison of distinct pointer types lacks a cast
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2  -c fixNS.c -o fixNS.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2  -c libxmlFeatures.c -o libxmlFeatures.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 ->>>>>>>
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2  -c xmlsecurity.c -o xmlsecurity.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2  -c xpath.c -o xpath.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -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 -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/XML/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (XML)

The downloaded source packages are in
    ‘/private/var/folders/f_/7p8pfw9s5ps2yndz1yj3fsxc0000gn/T/RtmpkJkVzp/downloaded_packages’
Old packages: 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth',
  'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial',
  'survival'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Hmisc’ had non-zero exit status
> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘Hmisc’
In addition: Warning messages:
1: package ‘rtracklayer’ was built under R version 3.2.2 
2: package ‘GenomicRanges’ was built under R version 3.2.2 
3: package ‘S4Vectors’ was built under R version 3.2.2 
4: package ‘IRanges’ was built under R version 3.2.2 
5: In .recacheSubclasses(def@className, def, doSubclasses, env) :
  undefined subclass "externalRefMethod" of class "expressionORfunction"; definition not updated
6: In .recacheSubclasses(def@className, def, doSubclasses, env) :
  undefined subclass "externalRefMethod" of class "functionORNULL"; definition not updated
7: package ‘GenomeInfoDb’ was built under R version 3.2.2 
Error: package ‘Gviz’ could not be loaded

 

 

 

ADD COMMENTlink modified 2.2 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.2 years ago by ivonyao0
0
gravatar for Dan Tenenbaum
2.2 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

Try this:

 

options(install.packages.compile.from.source="never")
library(BiocInstaller)
biocLite('cummeRbund')

See if that works.

It seems like what's happening now is R is deciding to install a source package over an older binary package and not giving you the option to disable this, and the compilation fails because you don't have gfortran installed.

Dan

ADD COMMENTlink written 2.2 years ago by Dan Tenenbaum ♦♦ 8.2k
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