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 escribi?: > 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 Fern?ndez Bay?n <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 aqu? > > > > > > > ../inst/include/RcppEigenWrap.h:203:17: error: no hay una funci?n > > > > > > > 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 aqu? > > > > > > > ../inst/include/RcppEigenWrap.h:169:17: error: no hay una funci?n > > > > > > > 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]] > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Bioconductor mailing list > > > > > > > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) > > > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > Search the archives: > > > > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Bioconductor mailing list > > > > > > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) > > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > Search the archives: > > > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Bioconductor mailing list > > > > > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > Search the archives: > > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > > > > > > > -- > > > > Computational Biology / Fred Hutchinson Cancer Research Center > > > > 1100 Fairview Ave. N. > > > > PO Box 19024 Seattle, WA 98109 > > > > > > > > Location: Arnold Building M1 B861 > > > > Phone: (206) 667-2793 > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > -- > > A model is a lie that helps you see the truth. > > > > Howard Skipper > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor