Re: [Bioc-devel] affycoretools in devel failed to install

Tue, 05 Aug 2014 07:16:02 -0700 

I do confirm smooth installation of the affycoretools package.
Thank you!

install log:
> biocLite("affycoretools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'affycoretools'
trying URL '
http://bioconductor.org/packages/3.0/bioc/src/contrib/affycoretools_1.37.3.tar.gz
'
Content type 'application/x-gzip' length 6911561 bytes (6.6 Mb)
opened URL
==================================================
downloaded 6.6 Mb

* installing *source* package ‘affycoretools’ ...
** R
** inst
** preparing package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc,  :
  No generic function found corresponding to requested imported methods for
"colnames<-" from package "annaffy" (malformed exports?)
** help
Warning:
/tmp/Rtmp9ynorH/R.INSTALL14a7ce64ed3/affycoretools/man/fixHeaderAndGo.Rd:16:
unexpected RCODE '
', expecting '{'
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc,  :
  No generic function found corresponding to requested imported methods for
"colnames<-" from package "annaffy" (malformed exports?)
* DONE (affycoretools)


2014-07-29 16:04 GMT+02:00 Dan Tenenbaum <dtene...@fhcrc.org>:

>
>
> ----- Original Message -----
> > From: "Vojtech Kulvait" <kulv...@gmail.com>
> > To: bioc-devel@r-project.org
> > Sent: Tuesday, July 29, 2014 4:40:36 AM
> > Subject: Re: [Bioc-devel] affycoretools in devel failed to install
> >
> > Looks like I was right :)
> >
> >
> > 2014-07-29 13:15 GMT+02:00 Martin Morgan <mtmor...@fhcrc.org>:
> >
> > > Looks like Dan corrected symbols2indices then Jim made an
> > > additional change
> > >
> > >
> ------------------------------------------------------------------------
> > > r91908 | jmacdon | 2014-06-26 13:16:03 -0700 (Thu, 26 Jun 2014) | 1
> > > line
> > >
> > > Converted to use roxygen2, so all Rd files changed. Also
> > > generalized
> > > vennSelect2 so it will work with non-Affy data. Added functions to
> > > create
> > > tables from GO analyses using ReportingTools.
> > >
> ------------------------------------------------------------------------
> > > r91900 | d.tenenbaum | 2014-06-26 10:47:24 -0700 (Thu, 26 Jun 2014)
> > > | 3
> > > lines
> > >
> > > replace symbols2indices throughout with ids2indices as limma
> > > has renamed this function.
> > >
> > >
> > > ... but Jim bumped the version in the wrong direction so Dan's
> > > commit
> > > never made it to the build system, and the 'latest' version is the
> > > version
> > > before Dan's.
> > >
> > > $ svn diff -c91908 DESCRIPTION
> > > Index: DESCRIPTION
> > > ===================================================================
> > > --- DESCRIPTION (revision 91907)
> > > +++ DESCRIPTION (revision 91908)
> > > @@ -2,7 +2,7 @@
> > >  Date: 2008-12-15
> > >  Title: Functions useful for those doing repetitive analyses
> > >      with Affymetrix GeneChips.
> > > -Version: 1.37.2
> > > +Version: 1.35.10
> > >
> > >
> > >
>
> I've bumped it to 1.37.3, so these changes should go through.
>
> Thanks,
> Dan
>
>
> > > On 07/29/2014 03:35 AM, Vojtech Kulvait wrote:
> > >
> > >> This do not help either:
> > >>
> > >>  BiocInstaller::biocLite("limma", type="source")
> > >>>
> > >> BioC_mirror: http://bioconductor.org
> > >> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> > >> 3.1.1.
> > >> Installing package(s) 'limma'
> > >> trying URL '
> > >> http://bioconductor.org/packages/3.0/bioc/src/contrib/
> > >> limma_3.21.10.tar.gz'
> > >> Content type 'application/x-gzip' length 1215791 bytes (1.2 Mb)
> > >> opened URL
> > >> ==================================================
> > >> downloaded 1.2 Mb
> > >>
> > >> * installing *source* package ‘limma’ ...
> > >>
> > >> ** libs
> > >> gcc -std=gnu99 -I/usr/local/lib/R-3.1.1/include -DNDEBUG
> > >> -I/usr/local/include    -fpic  -g -O2  -c normexp.c -o normexp.o
> > >> gcc -std=gnu99 -I/usr/local/lib/R-3.1.1/include -DNDEBUG
> > >> -I/usr/local/include    -fpic  -g -O2  -c weighted_lowess.c -o
> > >> weighted_lowess.o
> > >> gcc -std=gnu99 -shared -L/usr/local/lib -o limma.so normexp.o
> > >> weighted_lowess.o -L/usr/local/lib/R-3.1.1/lib -lR
> > >> installing to /usr/local/lib/R-3.1.1/library/limma/libs
> > >> ** R
> > >> ** inst
> > >> ** preparing package for lazy loading
> > >> ** help
> > >> *** installing help indices
> > >> ** building package indices
> > >> ** installing vignettes
> > >> ** testing if installed package can be loaded
> > >> * DONE (limma)
> > >>
> > >> The downloaded source packages are in
> > >>      ‘/tmp/RtmpjACGfx/downloaded_packages’
> > >>
> > >> Updating HTML index of packages in '.Library'
> > >> Making 'packages.html' ... done
> > >>
> > >>> BiocInstaller::biocLite("affycoretools")
> > >>>
> > >> BioC_mirror: http://bioconductor.org
> > >> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> > >> 3.1.1.
> > >> Installing package(s) 'affycoretools'
> > >> trying URL '
> > >> http://bioconductor.org/packages/3.0/bioc/src/contrib/
> > >> affycoretools_1.37.1.tar.gz
> > >> '
> > >> Content type 'application/x-gzip' length 6909574 bytes (6.6 Mb)
> > >> opened URL
> > >> ==================================================
> > >> downloaded 6.6 Mb
> > >>
> > >> * installing *source* package ‘affycoretools’ ...
> > >> ** R
> > >> ** inst
> > >> ** preparing package for lazy loading
> > >> Error : object ‘symbols2indices’ is not exported by
> > >> 'namespace:limma'
> > >> ERROR: lazy loading failed for package ‘affycoretools’
> > >> * removing ‘/usr/local/lib/R-3.1.1/library/affycoretools’
> > >>
> > >
> > > I don't think the complaint is about affycoretools
> > >
> > >>
> > >> The downloaded source packages are in
> > >>      ‘/tmp/RtmpjACGfx/downloaded_packages’
> > >>
> > >> Updating HTML index of packages in '.Library'
> > >> Making 'packages.html' ... done
> > >> Warning message:
> > >> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> > >>    installation of package ‘affycoretools’ had non-zero exit
> > >>    status
> > >>
> > >>
> > >>
> > >>
> > >> 2014-07-29 12:32 GMT+02:00 Vojtech Kulvait <kulv...@gmail.com>:
> > >>
> > >>  Hi,
> > >>> thank you for your replies. I am sending full output of my R
> > >>> session
> > >>> started few minutes ago.
> > >>> The problem is still remaining.
> > >>> Best,
> > >>> Vojtech.
> > >>>
> > >>> R version 3.1.1 (2014-07-10) -- "Sock it to Me"
> > >>> Copyright (C) 2014 The R Foundation for Statistical Computing
> > >>> Platform: x86_64-unknown-linux-gnu (64-bit)
> > >>>
> > >>> R is free software and comes with ABSOLUTELY NO WARRANTY.
> > >>> You are welcome to redistribute it under certain conditions.
> > >>> Type 'license()' or 'licence()' for distribution details.
> > >>>
> > >>>    Natural language support but running in an English locale
> > >>>
> > >>> R is a collaborative project with many contributors.
> > >>> Type 'contributors()' for more information and
> > >>> 'citation()' on how to cite R or R packages in publications.
> > >>>
> > >>> Type 'demo()' for some demos, 'help()' for on-line help, or
> > >>> 'help.start()' for an HTML browser interface to help.
> > >>> Type 'q()' to quit R.
> > >>>
> > >>>  library(BiocInstaller)
> > >>>>
> > >>> Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite for
> > >>> help
> > >>>
> > >>>>   BiocInstaller::biocValid()
> > >>>>
> > >>> [1] TRUE
> > >>>
> > >>>> BiocInstaller::biocLite()
> > >>>>
> > >>> BioC_mirror: http://bioconductor.org
> > >>> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> > >>> 3.1.1.
> > >>>
> > >>>> BiocInstaller::biocLite("affycoretools")
> > >>>>
> > >>> BioC_mirror: http://bioconductor.org
> > >>> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> > >>> 3.1.1.
> > >>> Installing package(s) 'affycoretools'
> > >>> trying URL '
> > >>> http://bioconductor.org/packages/3.0/bioc/src/contrib/
> > >>> affycoretools_1.37.1.tar.gz
> > >>> '
> > >>> Content type 'application/x-gzip' length 6909574 bytes (6.6 Mb)
> > >>> opened URL
> > >>> ==================================================
> > >>> downloaded 6.6 Mb
> > >>>
> > >>> * installing *source* package ‘affycoretools’ ...
> > >>>
> > >>> ** R
> > >>> ** inst
> > >>> ** preparing package for lazy loading
> > >>> Error : object ‘symbols2indices’ is not exported by
> > >>> 'namespace:limma'
> > >>> ERROR: lazy loading failed for package ‘affycoretools’
> > >>> * removing ‘/usr/local/lib/R-3.1.1/library/affycoretools’
> > >>>
> > >>>
> > >>> The downloaded source packages are in
> > >>>      ‘/tmp/RtmpjACGfx/downloaded_packages’
> > >>>
> > >>> Updating HTML index of packages in '.Library'
> > >>> Making 'packages.html' ... done
> > >>> Warning message:
> > >>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> > >>>    installation of package ‘affycoretools’ had non-zero 
> > >>> exit
> > >>>    status
> > >>>
> > >>>  sessionInfo()
> > >>>>
> > >>> R version 3.1.1 (2014-07-10)
> > >>> Platform: x86_64-unknown-linux-gnu (64-bit)
> > >>>
> > >>> locale:
> > >>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> > >>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> > >>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> > >>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> > >>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > >>>
> > >>> attached base packages:
> > >>> [1] stats     graphics  grDevices utils     datasets  methods
> > >>>   base
> > >>>
> > >>> other attached packages:
> > >>> [1] BiocInstaller_1.15.5
> > >>>
> > >>> loaded via a namespace (and not attached):
> > >>> [1] tools_3.1.1
> > >>>
> > >>>>
> > >>>>
> > >>>
> > >>>
> > >>> 2014-07-25 17:28 GMT+02:00 Martin Morgan <mtmor...@fhcrc.org>:
> > >>>
> > >>> On 07/25/2014 04:32 AM, Vojtech Kulvait wrote:
> > >>>
> > >>>>
> > >>>>  Hello,
> > >>>>> when I try to install affycoretools in devel i get an error:
> > >>>>>
> > >>>>> * installing *source* package 
> > >>>>> ‘affycoretools’ ...
> > >>>>>
> > >>>>>
> > >>>>> ** R
> > >>>>> ** inst
> > >>>>> ** preparing package for lazy loading
> > >>>>> Error : object ‘symbols2indices’ is 
> > >>>>> not exported
> > >>>>> by
> > >>>>> 'namespace:limma'
> > >>>>> ERROR: lazy loading failed for package
> > >>>>> ‘affycoretools’
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> I think I have up to date instalation of all packages.
> > >>>>>
> > >>>>>
> > >>>> Hi Vojtech -- just to add to the advice, you can use
> > >>>>
> > >>>>    BiocInstaller::biocValid()
> > >>>>
> > >>>> to check your installation,
> > >>>>
> > >>>>    BiocInstaller::biocLite()
> > >>>>
> > >>>> to update your current packages.
> > >>>>
> > >>>> Martin
> > >>>>
> > >>>>
> > >>>>   Vojtech.
> > >>>>
> > >>>>>
> > >>>>>          [[alternative HTML version deleted]]
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> _______________________________________________
> > >>>>> Bioc-devel@r-project.org mailing list
> > >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>> --
> > >>>> 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
> > >>>>
> > >>>>
> > >>>
> > >>>
> > >>         [[alternative HTML version deleted]]
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Bioc-devel@r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >>
> > >
> > > --
> > > 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
> > >
> >
> >       [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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