Hi Vincent, sorry I only realized now that the error was below the deprecate message:
org.Hs.egCHRLOC is deprecated as the data is better accessed from another location. Please use an appropriate TxDb object or package for this kind of data. LaTeX errors: !pdfTeX error: /usr/bin/pdflatex (file ./coverage1.pdf): PDF inclusion: require d page does not exist <0> ==> Fatal error occurred, no output PDF file produced! Calls: <Anonymous> -> texi2pdf -> texi2dvi Execution halted The error comes from LaTeX, however chimera package version 1.7.19 was correctly built on 2014-08-22 Since that time I did not made any changes and I do not understand where is the issue. Cheers Raf On 23/09/14 12:41, Vincent Carey wrote: > Of note, this is not an error and seems at this time not even to be a > warning. > A message is emitted indicating the deprecation, so we have a release to > figure out how to deal with the fact that the *CHR/*CHRLOC entities will go > away > in the next release. > > There are various possible workarounds. Some more commentary will be > forthcoming. > > > On Tue, Sep 23, 2014 at 3:52 AM, calogero UNITO <raffaele.calog...@unito.it> > wrote: > >> Hi, >> I am the maintainer of chimera package and I am getting the following >> error in the develop version: >> >> org.Hs.egCHRLOC is deprecated as the data is better accessed from >> another location. Please use an appropriate TxDb object or package for >> this kind of data. >> >> Could please indicate me which package I should used instead of >> org.Hs.eg.db ? >> >> Cheers >> Raf >> >> -- >> ---------------------------------------- >> Prof. Raffaele A. Calogero >> Bioinformatics and Genomics Unit >> MBC Centro di Biotecnologie Molecolari >> Via Nizza 52, Torino 10126 >> Tel. ++39 0116706457 >> Fax ++39 0112366457 >> Mobile ++39 3333827080 >> email: raffaele.calog...@unito.it >> raffaele.calog...@gmail.com >> www: http://www.bioinformatica.unito.it >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 Tel. ++39 0116706457 Fax ++39 0112366457 Mobile ++39 3333827080 email: raffaele.calog...@unito.it raffaele.calog...@gmail.com www: http://www.bioinformatica.unito.it [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
