[BioC] Weird things happening with minfi and RcppEigen

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Nov 29 19:37:39 CET 2012 

On Thu, Nov 29, 2012 at 1:26 PM, Tim Triche, Jr. <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 ) 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> 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> 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> 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>
>> >>> 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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>> >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >>>>
>> >>>
>> >>>          [[alternative HTML version deleted]]
>> >>>
>> >>>
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>> >>
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>> >
>> >
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