[BioC] Weird things happening with minfi and RcppEigen
Gustavo Fernández Bayón
gbayon at gmail.com
Fri Nov 30 08:43:45 CET 2012
Hi.
Sorry for the late reply. Thank you all for the answers. Finally, I decided to go Kasper's way and roll back to 0.10.0. Everything is working fine now.
See you around,
Gustavo
---------------------------
Enviado con Sparrow (http://www.sparrowmailapp.com/?sig)
El jueves 29 de noviembre de 2012 a las 19:37, Kasper Daniel Hansen escribió:
> On Thu, Nov 29, 2012 at 1:26 PM, Tim Triche, Jr. <tim.triche at gmail.com (mailto:tim.triche at gmail.com)> wrote:
> > Will illuminaio allow crlmm to be decoupled from minfi?
>
>
>
> Yes, and that is why we don't have this problem in devel.
>
> Kasper
>
>
> > Because that might be a good thing, especially now that you've switched to
> > an SE subclass for real work.
> >
> > FWIW, revision 4048 and beyond of RcppEigen (from
> > svn://svn.r-forge.r-project.org/svnroot/rcpp/pkg/RcppEigen (http://svn.r-forge.r-project.org/svnroot/rcpp/pkg/RcppEigen) ) fixes the
> > glitch for both crlmm and (cc: Bob Carpenter for when his users start
> > fussing as well) the rstan package. Verified yesterday.
> >
> >
> >
> >
> > On Thu, Nov 29, 2012 at 6:46 AM, Kasper Daniel Hansen
> > <kasperdanielhansen at gmail.com (mailto:kasperdanielhansen at gmail.com)> wrote:
> > >
> > > "Unfortunately", I fixed this problem on my own system yesterday (or
> > > was it the day before) and I don't really want to restore it.
> > >
> > > For minfi, all that is being checked (I guess) is whether the
> > > namespace of crlmm can be accessed when it is loaded. We don't in any
> > > way depend on RcppEigen, and we also don't use any code from crlmm
> > > which depends on RcppEigen.
> > >
> > > Kasper
> > >
> > > On Thu, Nov 29, 2012 at 9:43 AM, Martin Morgan <mtmorgan at fhcrc.org (mailto:mtmorgan at fhcrc.org)> wrote:
> > > > On 11/29/2012 06:39 AM, Kasper Daniel Hansen wrote:
> > > > >
> > > > > Gustova, this all happens because minfi (in release) depends on crlmm
> > > > > which depends on RcppEigen. In bioc-devel, minfi does not depend on
> > > > > crlmm, so that is an easy fix for you.
> > > > >
> > > > > The issue here is that a couple of days ago, Rcpp 0.10.1 was released.
> > > > > This release broke RcppEigen, but for various reasons, Rcpp was still
> > > > > allowed to be installed to your system. The Rcpp(Eigen) people are
> > > > > working on a fix, but for now, the solution is to roll back Rcpp to
> > > > > version 0.10.0.
> > > >
> > > >
> > > >
> > > >
> > > > There's still some mystery going on, though, as Gustavo did
> > > >
> > > > library(minfi)
> > > >
> > > > which failed, and then in the same session
> > > >
> > > > library(minfi)
> > > >
> > > > which worked.
> > > >
> > > > Maybe the DLL whose symbol couldn't be found, and prevented RcppEigen
> > > > from
> > > > loading, was not properly removed when RcppEigen failed?
> > > >
> > > > Martin
> > > >
> > > >
> > > > >
> > > > > The same issue/solution is true for crlmm users btw.
> > > > >
> > > > > I expect this to be solved in a couple of days. I reported this to
> > > > > the Rcpp developers and they claim they have fixed RcppEigen in their
> > > > > subversion repository. After this has been confirmed, they have to
> > > > > make a new release of RcppEigen, which should not be that hard.
> > > > >
> > > > > For interested lurkers, RcppArmadillo breaks with the same error as
> > > > > RcppEigen, but the error with RcppArmadillo can be fixed by
> > > > > reinstalling RcppArmadillo after Rcpp 0.10.1 has been installed.
> > > > >
> > > > > Kasper
> > > > >
> > > > > On Thu, Nov 29, 2012 at 7:19 AM, Benilton Carvalho
> > > > > <beniltoncarvalho at gmail.com (mailto:beniltoncarvalho at gmail.com)> wrote:
> > > > > >
> > > > > > 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 at gmail.com (mailto:gbayon at 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
> > > > > > >
> > > > > > > [[alternative HTML version deleted]]
> > > > > > >
> > > > > > >
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