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[Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1

7 messages · Ludwig Geistlinger, Martin Morgan, Rainer Johannes +1 more

Original
Ludwig Geistlinger
# 
Hi,

I am experiencing troubles installing "Hmisc", especially its dependency
"acepack", via
in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded
from https://r.research.att.com/.

The error reads:


BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable)
  (2015-11-16 r69640).
Installing package(s) ?acepack?
Paket, das nur als Quelltext vorliegt und eventuell ?bersetzung von
  C/C++/Fortran ben?tigt.: ?acepack?
Do you want to attempt to install these from sources?
y/n: y
installing the source package ?acepack?

versuche URL 'https://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz'
Content type 'application/x-gzip' length 33590 bytes (32 KB)
==================================================
downloaded 32 KB

* installing *source* package ?acepack? ...
** Paket ?acepack? erfolgreich entpackt und MD5 Summen ?berpr?ft
** libs
gfortran-4.8   -fPIC  -g -O2  -c ace.f -o ace.o
make: gfortran-4.8: No such file or directory
make: *** [ace.o] Error 1
ERROR: compilation failed for package ?acepack?
* removing
?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/acepack?


which indicates that "gfortran-4.8" is missing.
I have however installed the recommended "gfortran-5.2" for El Capitan
from here:

https://gcc.gnu.org/wiki/GFortranBinaries#MacOS

Yesterday, I tried quite some time to install 4.8-versions of gfortran
available from the website above, however they are not compatible with El
Capitan (Error reads: kern.osversion not recognized: ?15.0.0) and searched
through several newsgroups reporting on that issue, I was however not able
to fix that.

Did anyone of the community here experienced similar issues and have some
suggestions for me!?

Thank you very much!

Best,
Ludwig
Rainer Johannes
# 
Dear Ludwig,

I tried to install that package and it compiled nicely on my system with
R Under development (unstable) (2015-10-20 r69547)
Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

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_1.21.1

loaded via a namespace (and not attached):
[1] tools_3.3.0


I?m installing the fortran through homebrew, actually, fortran is part of the gcc ?bottle? there, thus I installed
brew install gcc

and I?m building and compiling R always from source with:

/configure SHELL='/bin/bash' \
	    --prefix=$PREFIX \
	    r_arch=x86_64 \
	    --x-includes=/usr/X11/include/ \
	    --x-libraries=/usr/X11/lib/ \
	    CC="clang" \
	    CXX="clang++" \
	    OBJC="clang" \
	    F77="gfortran -arch x86_64" \
	    FC="gfortran -arch x86_64" \
	    --with-system-zlib \
	    --with-blas='-framework Accelerate' \
	    --with-lapack \
	    CPPFLAGS="-D__ACCELERATE__  \
	    --enable-R-framework=no \
	    --enable-memory-profiling \
	    --enable-R-shlib


I never had any problems anymore with missing fortran compilers on OS X

Hope that helps,

cheers, jo
Ludwig Geistlinger
# 
While I am following Jo's suggestions on installing gcc via homebrew on my
mac laptop (is it normal that the "make bootstrap" command takes >20 min
already?), I am in parallel trying to make R/Bioc-devel working on our
institutional linux machines.

I was able to configure/make R-devel here, however when running biocLite()
I am encountering (I wonder whether this should be a new thread!?):
Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable)
  (2015-11-16 r69640).
Installing package(s) ?Biobase?, ?IRanges?, ?AnnotationDbi?
also installing the dependencies ?BiocGenerics?, ?S4Vectors?

trying URL
'https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocGenerics_0.17.1.tar.gz'
Content type 'unknown' length 38319 bytes (37 KB)
==================================================
downloaded 37 KB

trying URL
'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.9.tar.gz'
Content type 'unknown' length 204430 bytes (199 KB)
==================================================
downloaded 199 KB

trying URL
'https://bioconductor.org/packages/3.3/bioc/src/contrib/Biobase_2.31.0.tar.gz'
Content type 'unknown' length 1671264 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL
'https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.5.5.tar.gz'
Content type 'unknown' length 490192 bytes (478 KB)
==================================================
downloaded 478 KB

trying URL
'https://bioconductor.org/packages/3.3/bioc/src/contrib/AnnotationDbi_1.33.1.tar.gz'
Content type 'unknown' length 4268223 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ?BiocGenerics? ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ?append? in package ?BiocGenerics?
Creating a new generic function for ?as.data.frame? in package ?BiocGenerics?
Error in setGeneric("as.vector", signature = "x") :
  ?as.vector? dispatches internally;  methods can be defined, but the
generic function is implicit, and cannot be changed.
Error : unable to load R code in package ?BiocGenerics?
ERROR: lazy loading failed for package ?BiocGenerics?
* removing ?/home/users/geistlinger/R/R-devel/library/BiocGenerics?
ERROR: dependency ?BiocGenerics? is not available for package ?S4Vectors?
* removing ?/home/users/geistlinger/R/R-devel/library/S4Vectors?
ERROR: dependency ?BiocGenerics? is not available for package ?Biobase?
* removing ?/home/users/geistlinger/R/R-devel/library/Biobase?
ERROR: dependencies ?BiocGenerics?, ?S4Vectors? are not available for
package ?IRanges?
* removing ?/home/users/geistlinger/R/R-devel/library/IRanges?
ERROR: dependencies ?BiocGenerics?, ?Biobase?, ?IRanges?, ?S4Vectors? are
not available for package ?AnnotationDbi?
* removing ?/home/users/geistlinger/R/R-devel/library/AnnotationDbi?

The downloaded source packages are in
        ?/tmp/Rtmpx7szqQ/downloaded_packages?
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ?BiocGenerics? had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ?S4Vectors? had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ?Biobase? had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ?IRanges? had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ?AnnotationDbi? had non-zero exit status


Any suggestions here as well? Thanks!
R Under development (unstable) (2015-11-16 r69640)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: SUSE Linux Enterprise Desktop 12

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=C                  LC_COLLATE=C
 [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_1.21.1

loaded via a namespace (and not attached):
[1] tools_3.3.0

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Rainer Johannes
    

    

      
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Could be that gcc via homebrew takes a while? especially if it is compiling that stuff from source?

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Henrik Bengtsson
    

    

      
      #
    

  


  

      
For your Linux problem:

You might have build R differently from what you had in the past, e.g.
static vs dynamic.

Try to explicitly re-install those failed dependences and see if you any
further.  If so, you might wanna remove all your installed packages and
start over with a fresh package library setup.

Just an idea

Henrik
On Nov 18, 2015 05:47, "Ludwig Geistlinger" <

        
Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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The suggestion on R-SIG-mac in the thread I cited is that homebrew is not the right way to go. This is from very established members of the R-community (Simon Urbanek, Brian Ripley), and I would not treat it lightly.

Also, if you are installing R-devel (implied by use of Bioc 3.3), there are some recent commits (from Michael Lawrence, involving method dispatch) that might be causing problems; you'll definitely want the head of svn trunk rather than a snapshot.

Martin