Roll back Rcpp to 0.10.0, then reinstall RcppEigen... Check if that helps
you out. b


On 29 November 2012 10:14, Gustavo Fernández Bayón <gbayon@gmail.com> wrote:

> Hi everybody.
>
> I have updated some packages (RcppEigen, among others) after being asked
> by biocLite(). The process ended up with errors relating to the
> 'r_vector_start' template (I guess it's something about Rcpp or similar).
>
> If I try to reinstall RcppEigen, I get the following output:
>
>  > biocLite('RcppEigen')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'RcppEigen'
> probando la URL 'http://cran.fhcrc.org/src/contrib/RcppEigen_0.3.1.tar.gz'
> Content type 'application/x-gzip' length 1057901 bytes (1.0 Mb)
> URL abierta
> ==================================================
> downloaded 1.0 Mb
>
> * installing *source* package 'RcppEigen' ...
> ** package 'RcppEigen' successfully unpacked and MD5 sums checked
> ** libs
> g++ -I/usr/share/R/include -DNDEBUG
> -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic
> -O3 -pipe -g -c RcppEigen.cpp -o RcppEigen.o
> g++ -I/usr/share/R/include -DNDEBUG
> -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic
> -O3 -pipe -g -c fastLm.cpp -o fastLm.o
> In file included from ../inst/include/RcppEigen.h:27:0,
> from fastLm.h:25,
> from fastLm.cpp:23:
> ../inst/include/RcppEigenWrap.h: En el constructor
> 'Rcpp::traits::Exporter<Eigen::Map<Eigen::Matrix<_Scalar,
> -0x00000000000000001, -0x00000000000000001> > >::Exporter(SEXP) [with T
> = double, SEXP = SEXPREC*]':
> /usr/local/lib/R/site-library/Rcpp/include/Rcpp/as.h:55:51: instanciado
> desde 'T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag)
> [with T = Eigen::Map<Eigen::Matrix<double, -0x00000000000000001,
> -0x00000000000000001>, 0, Eigen::Stride<0, 0> >, SEXP = SEXPREC*]'
> /usr/local/lib/R/site-library/Rcpp/include/Rcpp/as.h:100:89: instanciado
> desde 'T Rcpp::as(SEXP) [with T = Eigen::Map<Eigen::Matrix<double,
> -0x00000000000000001, -0x00000000000000001>, 0, Eigen::Stride<0, 0> >,
> SEXP = SEXPREC*]'
> fastLm.cpp:207:50: instanciado desde aquí
> ../inst/include/RcppEigenWrap.h:203:17: error: no hay una función
> coincidente para la llamada a 'r_vector_start(SEXPREC*&)'
> ../inst/include/RcppEigenWrap.h:203:17: nota: el candidato es:
> /usr/local/lib/R/site-library/Rcpp/include/Rcpp/internal/r_vector.h:30:51:
> nota: template<int RTYPE> typename Rcpp::traits::storage_type::type*
> Rcpp::internal::r_vector_start(SEXP)
> ../inst/include/RcppEigenWrap.h: En el constructor
> 'Rcpp::traits::Exporter<Eigen::Map<Eigen::Matrix<_Scalar,
> -0x00000000000000001, 1> > >::Exporter(SEXP) [with T = double, SEXP =
> SEXPREC*]':
> /usr/local/lib/R/site-library/Rcpp/include/Rcpp/as.h:55:51: instanciado
> desde 'T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag)
> [with T = Eigen::Map<Eigen::Matrix<double, -0x00000000000000001, 1>, 0,
> Eigen::Stride<0, 0> >, SEXP = SEXPREC*]'
> /usr/local/lib/R/site-library/Rcpp/include/Rcpp/as.h:100:89: instanciado
> desde 'T Rcpp::as(SEXP) [with T = Eigen::Map<Eigen::Matrix<double,
> -0x00000000000000001, 1>, 0, Eigen::Stride<0, 0> >, SEXP = SEXPREC*]'
> fastLm.cpp:208:50: instanciado desde aquí
> ../inst/include/RcppEigenWrap.h:169:17: error: no hay una función
> coincidente para la llamada a 'r_vector_start(SEXPREC*&)'
> ../inst/include/RcppEigenWrap.h:169:17: nota: el candidato es:
> /usr/local/lib/R/site-library/Rcpp/include/Rcpp/internal/r_vector.h:30:51:
> nota: template<int RTYPE> typename Rcpp::traits::storage_type::type*
> Rcpp::internal::r_vector_start(SEXP)
> make: *** [fastLm.o] Error 1
> ERROR: compilation failed for package 'RcppEigen'
> * removing '/usr/local/lib/R/site-library/RcppEigen'
> * restoring previous '/usr/local/lib/R/site-library/RcppEigen'
>
> The downloaded source packages are in
> '/tmp/RtmpZjWHiE/downloaded_packages'
> Mensajes de aviso perdidos
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package 'RcppEigen' had non-zero exit status
>
> I am sorry for the Spanish messages. The error is something like "There
> is no coincident function for the call to 'r_vector_start'".
>
> Afterwards, from a clean R session, something strange happens with
> minfi. If I try to load the package, underlying broken RcppEigen complains:
>
>  > library(minfi)
> Loading required package: BiocGenerics
> [...]
> Loading required package: Biostrings
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/usr/local/lib/R/site-library/RcppEigen/libs/RcppEigen.so':
> /usr/local/lib/R/site-library/RcppEigen/libs/RcppEigen.so: undefined
> symbol: _ZN4Rcpp8internal14r_vector_startILi10EiEEPT0_P7SEXPREC
> Error: package/namespace load failed for 'minfi'
>
> But, if I try to reload it again inmediately, surprise, surprise...
>
>  > library(minfi)
> Loading package bit 1.1-9
> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
> creators: bit bitwhich
> coercion: as.logical as.integer as.bit as.bitwhich which
> operator: ! & | xor != ==
> querying: print length any all min max range sum summary
> bit access: length<- [ [<- [[ [[<-
> for more help type ?bit
> Loading package ff2.2-10
> - getOption("fftempdir")=="/tmp/RtmpNZWjJl"
>
> - getOption("ffextension")=="ff"
>
> - getOption("ffdrop")==TRUE
>
> - getOption("fffinonexit")==TRUE
>
> - getOption("ffpagesize")==65536
>
> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your
> system stalls on large writes
>
> - getOption("ffbatchbytes")==16777216 -- consider a different value for
> tuning your system
>
> - getOption("ffmaxbytes")==536870912 -- consider a different value for
> tuning your system
>
>
> ...it loads minfi without problems. This is quite strange for me.
> Anyway, I have found some info in
>
> http://permalink.gmane.org/gmane.comp.lang.r.rcpp/4404
>
> that maybe explains why everything has broken, but the strange thing
> with minfi still shocks me a little bit. Is there any reason for this?
> Any solution I can use to restore my library (specially minfi) to a
> usable state, so I can continue executing my workflows?
>
> What follows is the output of sessionInfo():
>
>  > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8
> [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] minfi_1.4.0 Biostrings_2.26.2 GenomicRanges_1.10.5
> [4] IRanges_1.16.4 reshape_0.8.4 plyr_1.7.1
> [7] lattice_0.20-10 Biobase_2.18.0 BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.26.0 annotate_1.36.0 AnnotationDbi_1.20.3
> [4] beanplot_1.1 BiocInstaller_1.8.3 bit_1.1-9
> [7] codetools_0.2-8 crlmm_1.16.9 DBI_0.2-5
> [10] ellipse_0.3-7 ff_2.2-10 foreach_1.4.0
> [13] genefilter_1.40.0 grid_2.15.2 iterators_1.0.6
> [16] limma_3.14.2 MASS_7.3-22 Matrix_1.0-10
> [19] matrixStats_0.6.2 mclust_4.0 multtest_2.14.0
> [22] mvtnorm_0.9-9993 nor1mix_1.1-3 oligoClasses_1.20.0
> [25] parallel_2.15.2 preprocessCore_1.20.0 RColorBrewer_1.0-5
> [28] RcppEigen_0.3.1 R.methodsS3_1.4.2 RSQLite_0.11.2
> [31] siggenes_1.32.0 splines_2.15.2 stats4_2.15.2
> [34] survival_2.36-14 XML_3.95-0.1 xtable_1.7-0
> [37] zlibbioc_1.4.0
>
>
> Regards,
> Gus
>
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>
>
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