[BioC] Error installing impute package

Sat Jun 14 03:28:01 CEST 2014

----- Original Message -----
> From: "Peter Langfelder" <peter.langfelder at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Levi Waldron" <levi.waldron at hunter.cuny.edu>, "Stephanie M. Gogarten" <sdmorris at u.washington.edu>,
> bioconductor at r-project.org
> Sent: Friday, June 13, 2014 5:35:38 PM
> Subject: Re: [BioC] Error installing impute package
> 
> Hi all,
> 
> Simon already installed impute on the Mavericks machine, per my
> request. I just submitted a new version of WGCNA to CRAN and it
> should
> be up in a day or two, hopefully including the Mavericks binary.
> 
> To the best of my knowledge Bioconductor packages are not necessarily
> all installed on all CRAN machines, sometimes one has to ask for it
> specifically.
> 

Normally any dependency you specify in your DESCRIPTION file will be installed by both the BioC and CRAN build machines. Because we didn't have Mavericks builds at the beginning of our devel cycle, Simon has been installing some packages by hand, and not installing others (such as packages in Suggests). Most BioC packages are now building on Mavericks, and I'll contact the maintainers of the remaining ones to see how we can get them green. It's better for all concerned if packages are installed automatically and we don't have to make special requests.

Dan

> Best,
> 
> Peter
> 
> 
> 
> On Fri, Jun 13, 2014 at 5:02 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
> wrote:
> > Hi Levi,
> >
> > ----- Original Message -----
> >> From: "Levi Waldron" <levi.waldron at hunter.cuny.edu>
> >> To: "Peter Langfelder" <peter.langfelder at gmail.com>
> >> Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Stephanie M. Gogarten"
> >> <sdmorris at u.washington.edu>,
> >> bioconductor at r-project.org
> >> Sent: Thursday, June 12, 2014 6:22:47 PM
> >> Subject: Re: [BioC] Error installing impute package
> >>
> >> I just noticed this problem myself - not with impute itself, but
> >> because WGCNA is not building in CRAN for Mavericks.  I guess CRAN
> >> doesn't have linkable URLs, but here is the error message on the
> >> WGCNA
> >> build check for Mavericks:
> >>
> >> using R version 3.1.0 Patched (2014-06-11 r65921)
> >> using platform: x86_64-apple-darwin13.1.0 (64-bit)
> >> using session charset: UTF-8
> >> checking for file 'WGCNA/DESCRIPTION' ... OK
> >> this is package 'WGCNA' version '1.34'
> >> checking package namespace information ... OK
> >> checking package dependencies ... ERROR
> >> Package required but not available: 'impute'
> >>
> >> Packages suggested but not available for checking:
> >> 'GO.db' 'org.Hs.eg.db' 'org.Mm.eg.db' 'AnnotationDbi' 'minet'
> >>
> >> See the information on DESCRIPTION files in the chapter 'Creating
> >> R
> >> packages' of the 'Writing R Extensions' manual.
> >>
> >>
> >
> > The url is
> >
> > http://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks/WGCNA-00check.html
> >
> > I have written to Simon Urbanek who is running the Mavericks CRAN
> > builds and asked him about this. impute is available on all
> > platforms so I don't think the problem is on the BioC end. That
> > build report also says that other BioC packages in WGCNA's
> > Suggests field are not available, but they all should be.
> >
> > Will let you know what I find out.
> >
> > Thanks,
> > Dan
> >
> >
> >> On Wed, Apr 10, 2013 at 6:55 PM, Peter Langfelder
> >> <peter.langfelder at gmail.com> wrote:
> >> > Thanks Dan and Stephanie,
> >> >
> >> > both solutions have worked.
> >> >
> >> > Best,
> >> >
> >> > Peter
> >> >
> >> >
> >> > On Wed, Apr 10, 2013 at 3:29 PM, Dan Tenenbaum
> >> > <dtenenba at fhcrc.org>
> >> > wrote:
> >> >> On Wed, Apr 10, 2013 at 3:08 PM, Stephanie M. Gogarten
> >> >> <sdmorris at u.washington.edu> wrote:
> >> >>> Is the error occurring just in the R GUI, or in any R session?
> >> >>>  I'm having a
> >> >>> similar problem with DNAcopy when I try to load in the R GUI,
> >> >>> but
> >> >>> it works
> >> >>> fine in the terminal or in Emacs.
> >> >>>
> >> >>
> >> >> I have the same results; I get the error in the GUI but not in
> >> >> the
> >> >> command line. So I have two workarounds:
> >> >>
> >> >> 1) Use the command line version of R for the time being; and
> >> >> 2) Start the GUI R like this:
> >> >>
> >> >> Open Terminal.app (in /Applications/Utilities)
> >> >>
> >> >> then paste the following:
> >> >> export
> >> >> DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib
> >> >> open /Applications/R.app
> >> >>
> >> >> Then loading the impute package should work. I need to get back
> >> >> to
> >> >> you
> >> >> with a better solution.
> >> >>
> >> >> Dan
> >> >>
> >> >>
> >> >>
> >> >>> This is what I get with the GUI:
> >> >>>> library(DNAcopy)
> >> >>>
> >> >>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> >> >>>   unable to load shared object
> >> >>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcopy/libs/DNAcopy.so':
> >> >>>
> >> >>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcopy/libs/DNAcopy.so,
> >> >>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
> >> >>>   Referenced from:
> >> >>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcopy/libs/DNAcopy.so
> >> >>>   Reason: image not found
> >> >>> Error: package or namespace load failed for 'DNAcopy'
> >> >>>> sessionInfo()
> >> >>> R version 3.0.0 (2013-04-03)
> >> >>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >> >>>
> >> >>> locale:
> >> >>> [1]
> >> >>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >> >>>
> >> >>> attached base packages:
> >> >>> [1] stats     graphics  grDevices utils     datasets  methods
> >> >>>   base
> >> >>>
> >> >>> other attached packages:
> >> >>> [1] BiocInstaller_1.10.0
> >> >>>
> >> >>> loaded via a namespace (and not attached):
> >> >>> [1] tools_3.0.0
> >> >>>
> >> >>> Stephanie
> >> >>>
> >> >>>
> >> >>> On 4/10/13 2:41 PM, Peter Langfelder wrote:
> >> >>>>
> >> >>>> Hello,
> >> >>>>
> >> >>>> a user of my (CRAN) package WGCNA which depends on impute has
> >> >>>> a
> >> >>>> problem installing impute on his Mac OSX 10.8.3 under R
> >> >>>> 3.0.0.
> >> >>>> The
> >> >>>> problem seems to be loading the compiled libary impute.so.
> >> >>>> Can
> >> >>>> anyone
> >> >>>> please suggest a solution? Below is a transcript of his
> >> >>>> session.
> >> >>>>
> >> >>>> Thanks,
> >> >>>>
> >> >>>> Peter
> >> >>>>
> >> >>>>> biocLite("impute", lib = .libPaths())
> >> >>>>
> >> >>>> BioC_mirror: http://bioconductor.org
> >> >>>> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R
> >> >>>> version 3.0.0.
> >> >>>> Installing package(s) 'impute'
> >> >>>> trying URL
> >> >>>> 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/impute_1.34.0.tgz'
> >> >>>> Content type 'application/x-gzip' length 652872 bytes (637
> >> >>>> Kb)
> >> >>>> opened URL
> >> >>>> ==================================================
> >> >>>> downloaded 637 Kb
> >> >>>>
> >> >>>>
> >> >>>> The downloaded binary packages are in
> >> >>>>
> >> >>>> /var/folders/x_/wps51c0n0tx33tx406_xt9n80000gn/T//Rtmpd8CN5X/downloaded_packages
> >> >>>>>
> >> >>>>> library(impute)
> >> >>>>
> >> >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> >> >>>>    unable to load shared object
> >> >>>>
> >> >>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute/libs/impute.so':
> >> >>>>
> >> >>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute/libs/impute.so,
> >> >>>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
> >> >>>>    Referenced from:
> >> >>>>
> >> >>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute/libs/impute.so
> >> >>>>    Reason: image not found
> >> >>>> Error: package or namespace load failed for 'impute'
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> Bioconductor mailing list
> >> >>>> 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
> >> >>> 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
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >>
> >> --
> >> Levi Waldron
> >> Assistant Professor of Biostatistics
> >> City University of New York School of Public Health, Hunter
> >> College
> >> 2180 3rd Ave Rm 538
> >> New York NY 10035-4003
> >> phone: 212-396-7747
> >> www.waldronlab.org
> >>
>