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Installing Bioconductor 1.5 on R 2.0 for OS X

8 messages · stefano iacus, Byron Ellis, Michael Redmond +1 more

Original
Michael Redmond
# 
I have a working version of R 2.0 with option packages installed on an 
OS X 10.3.5 system. Option packages were installed with install.binaries 
option and that seemed to work. Install using sources failed.

I tried installing bioconductor from sources and got mixed results (at 
best). Some packages failed to install (annotate, graph, Rgraphviz and 
maybe XML and possibly others). I also need to install arrayCGH to get 
DNAcopy. That uses the g77 compiler and failes with a mismatch of gcc 
library versions. I have g77 from fink.

Is there a install.binary option for bioconductor and some of the 
bioconductor contributed packages (specifically  arrayCGH)? If not now, 
when (if ever). If never, I may need some help to fix compile errors 
trying from source.

I am working on this for an Apple 4 node XServe to see if it can be used 
  under the iNquiry portal for R/Bioconductor applications.

Thanks
Mike Redmond
UW-Madison Statistics
stefano iacus
#
On Nov 2, 2004, at 11:11 PM, Michael Redmond wrote:

            

      
      
      
    

        
hi Michael,

what exactly fails? You should set up the system as it is explained in 
the FAQ and g77 is one issue.
Are you using the getbioC script ? BioC 1.4 needs R 1.9.1 and 1.5 (to 
be released) needs R 2.0.0. You cannot use bioc 1.5 with 1.9.x

            

      
      
      
    

        
I strongly suggest you one of the two options
1. build R from scratch eventually using fink stuff
2. remove any fink stuff, and use the cran binary of R 2.0.0.

            

      
      
      
    

        
you should report the error logs to let us to help with these. I'm 
currently testing the build of BioC 1.5 using getBioC.
I'll put results here and on the bioc-related lists.

stefano

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Byron Ellis
    

    

      
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On Nov 2, 2004, at 2:11 PM, Michael Redmond wrote:

        

            

      
      
      
    

        
You want the g77 from http://hpc.sourceforge.net---the fink g77 has 
never worked properly for me (actually, thats a general statement about 
fink for me :-) )

            

      
      
      
    

        
Jan De Leeuw usually wraps up the latest Bioconductor release into his 
"Batteries Included" version of R. I don't think there's a dedicated OS 
X machine doing binary builds anymore (IIRC, there used to be one doing 
the nightly smoke test). Unfortunately, OS X is probably the most 
finicky platform at the moment as well for that reason.

            

      
      
      
    

        
Ooh! Could you ping me off list about how thats working out for you? 
Our group has been considering one to serve some of internal 
computational needs---we're mostly curious about how much 
administration and configuration it requires. (i.e., do you just turn 
it on and go?)

            

      
      
      
    

        

      
      
    

        
---
Byron Ellis (ellis@stat.harvard.edu)
"Oook" -- The Librarian

  
  


  


      

    

    

      
      

        


  

        

      Michael Redmond
    

    

      
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Stefano,
I have R 2.0.0 and am working with BioC 1.5, so far from source. I 
really don't want to compile from source if I can help it, but I can try 
setting up per the FAQ. It sounds like I should not use fink binaries 
for g77, and that I can fairly easily change.

I attached a text file of the status/error messages I have gotten so far 
in the BioC/DNAcopy installs.

Thanks for the quick response...
Mike
---

        
stefano iacus wrote:

            

      
      
      
    

        

      
      
    

        
-------------- next part --------------
[1] "Installation complete"

            
        
widgetTools version 1.4.7
        DynDoc version 1.5.0
        tkWidgets version 1.5.20
        Biobase version 1.5.0
        affydata version 1.4.0
        affy version 1.5.8
        affyPLM version 1.2.5
        genefilter version 1.5.0
        Biostrings version 1.0.0
        matchprobes version 1.0.12
        multtest version 1.5.2
        annaffy version 1.0.11
        gcrma version 1.1.1
        makecdfenv version 1.4.8
        Ruuid version 1.5.0
        geneplotter version 1.5.0
        edd version 1.5.0
        ROC version 1.0.13
        marray version 1.5.25
        RMAGEML version 2.1.0
        siggenes version 1.2.11
        vsn version 1.5.0

            

      
      
      
    

        
hgu95av2cdf version 1.4.3
        hgu133acdf version 1.4.3
        hu6800cdf version 1.4.3

            

      
      
      
    

        
GO version 1.6.5
        KEGG version 1.6.5
        hgu95av2 version 1.6.5
        rae230a version 1.6.5
        hsahomology version 1.6.5
        xlahomology version 1.6.5
        zebrafish version 1.6.5
        xenopuslaevis version 1.6.5
        hu6800 version 1.6.5

            

      
      
      
    

        
hgu95av2probe version 1.0
        hu6800probe version 1.0
        rae230aprobe version 1.0

            

      
      
      
    

        
XML version 0.95-6
        XML version 0.95-6
        SparseM version 0.52
        XML version 0.95-6
        xtable version 1.2-4
        statmod version 1.1.0
        sma version 0.5.14
        limma version 1.8.6
        XML version 0.95-6
        pamr version 1.22

            

      
      
      
    

        
fibroEset version 1.0
        golubEsets version 1.0

Packages that were not updated:
        annotate
        annotate
        graph
        Rgraphviz
        annotate

You have downloaded a default set of packages.
If you wish to see other download options, please go to the URL:
http://www.bioconductor.org/faq.html#getBioC
There were 14 warnings (use warnings() to see them)

            

      
      
      
    

        
Warning messages:
1: Installation of package genefilter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
2: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
3: 
 Package annotate version 1.5.1 suggests genefilter
Package annotate version 1.5.1 suggests XML version >= 0.92-2 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions,   ...
4: Installation of package annaffy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
5: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
6: 
 Package annotate version 1.5.1 suggests XML version >= 0.92-2 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions,   ...
7: Installation of package SparseM had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
8: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
9: 
 Package graph version 1.5.0 suggests SparseM version >= 0.36
Package graph version 1.5.0 suggests XML 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions,   ...
10: 
 Package Rgraphviz version 1.5.0 depends on graph 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions,   ...
11: Installation of package geneplotter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
12: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
13: 
 Package annotate version 1.5.1 suggests XML version >= 0.92-2 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions,   ...
14: Installation of package pamr had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 

-----

            

      
      
      
    

        
Running getBioC version 1.2.68....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to bioconductor@stat.math.ethz.ch.

[1] "Attempting to download DNAcopy from http://www.bioconductor.org/repository/release1.5/package/Source"
[1] "Download complete."
[1] "Installing DNAcopy"
* Installing *source* package 'DNAcopy' ...
** libs
g77   -fno-common  -g -O2 -c changepoints.f -o changepoints.o
g77   -fno-common  -g -O2 -c prune.f -o prune.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c rshared.c -o rshared.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o DNAcopy.so changepoints.o prune.o rshared.o  -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin -lg2c -lSystem -lcc_dynamic -framework R
ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist
ld: can't locate file for: -lfrtbegin
make: *** [DNAcopy.so] Error 1
ERROR: compilation failed for package 'DNAcopy'
Note: You did not specify a download type.  Using a default value of: Source 
This will be fine for almost all users
 
Note: You did not specify a download type.  Using a default value of: Source 
This will be fine for almost all users
 
[1] "Attempting to download rmutil from http://www.bioconductor.org/repository/lindsey/"
[1] "Download complete."
[1] "Installing rmutil"
* Installing *source* package 'rmutil' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c cutil.c -o cutil.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c dist.c -o dist.o
g77   -fno-common  -g -O2 -c gettvc.f -o gettvc.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c romberg.c -o romberg.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c toms614.c -o toms614.o
gcc -bundle -flat_namespace -undefined suppress -o rmutil.so cutil.o dist.o gettvc.o romberg.o toms614.o -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin -lg2c -lSystem
ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist
ld: can't locate file for: -lfrtbegin
make: *** [rmutil.so] Error 1
ERROR: compilation failed for package 'rmutil'
Note: Package rmutil not found in any known repository. 
Note: Package repeated not found in any known repository. 
Note: You did not specify a download type.  Using a default value of: Source 
This will be fine for almost all users
 
[1] "Attempting to download rmutil from http://www.bioconductor.org/repository/lindsey/"
[1] "Download complete."
[1] "Installing rmutil"
* Installing *source* package 'rmutil' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c cutil.c -o cutil.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c dist.c -o dist.o
g77   -fno-common  -g -O2 -c gettvc.f -o gettvc.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c romberg.c -o romberg.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include   -fno-common  -g -O2 -c toms614.c -o toms614.o
gcc -bundle -flat_namespace -undefined suppress -o rmutil.so cutil.o dist.o gettvc.o romberg.o toms614.o -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin -lg2c -lSystem
ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist
ld: can't locate file for: -lfrtbegin
make: *** [rmutil.so] Error 1
ERROR: compilation failed for package 'rmutil'
** Removing '/Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/rmutil'
** Restoring previous '/Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/rmutil'
[1] "Attempting to download aCGH from http://www.bioconductor.org/repository/release1.5/package/Source"
[1] "Download complete."
[1] "Installing aCGH"
* Installing *source* package 'aCGH' ...
** R
** data
** demo
** inst
** preparing package for lazy loading

** help
 >>> Building/Updating help pages for package 'aCGH'
     Formats: text html latex example 
  aCGH                              text    html    latex   example
  aCGH.process                      text    html    latex   example
  aCGH.read.Sprocs                  text    html    latex   example
  aCGH.test                         text    html    latex   example
  clusterGenome                     text    html    latex   example
  colorectal                        text    html    latex   example
  computeSD.func                    text    html    latex
  find.genomic.events               text    html    latex
  find.hmm.states                   text    html    latex   example
  findAber.func                     text    html    latex
  findAmplif.func                   text    html    latex
  findOutliers.func                 text    html    latex
  findTrans.func                    text    html    latex
  gainLoss                          text    html    latex   example
  heatmap                           text    html    latex   example
  human.chrom.info.Jul03            text    html    latex
  impute.lowess                     text    html    latex   example
  mergeFunc                         text    html    latex
  plotFreqStat                      text    html    latex   example
  plotGenome                        text    html    latex   example
  plotHmmStates                     text    html    latex   example
  plotSummaryProfile                text    html    latex   example
  states.hmm.func                   text    html    latex
  summarize.clones                  text    html    latex   example
* DONE (aCGH)
chmod: /Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/R.css: Operation not permitted
[1] "Installation complete"

            
        
DNAcopy version 1.1.0
        aCGH version 1.1.4

            

      
      
      
    

        
rmutil version 1.0
        rmutil version 1.0

Packages that were not updated:
        repeated

Warning messages: 
1: Installation of package DNAcopy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
2: Installation of package rmutil had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
3: 
 Package repeated version 1.0 depends on rmutil 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions,  
4: Installation of package rmutil had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Michael Redmond
    

    

      
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Byron,
I will try the sourceforge g77 in place of the fink version. I am still 
hoping I can find someone that has prebuilt the BioC binaries I need.

It may be possible to run the XServe as a turnkey system, but for now it 
is going to be a fair amount of work to get R and Bioconductor into the 
portal interface. Once there, access is easy to manage. It is still 
likely that, even with the portal, some number of the research community 
here will want to run the XServe as a full Unix system, so then 
administation will be more typical of other systems.

Thanks
Mike
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Byron Ellis wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      stefano iacus
    

    

      
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On Nov 2, 2004, at 11:36 PM, Byron Ellis wrote:

        

            

      
      
      
    

        
well, for 1.4 there are binary builds. For 1.5 I'm late, but it should 
be me again.
I'll setup everything back soon.
stefano

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      elijah wright
    

    

      
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i have an extra (unused) OSX machine under my desk at school, if its not 
too hard to rig up automated binary builds....

are these getting done on other platforms, such that i could just gank the 
scripts and do the builds?

--elijah

  
  


  


      

    

    
5 days later

    

      
      

        


  

        

      Michael Redmond
    

    

      
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Byron,
I have been having some success with R installation by replacing the 
fink version of g77 with the sourceforge version. So thanks very much 
for that info.

Now that I have a good R base system compiled on OS X (I am trying  both 
on a Powerbook for testing and on the XServe), I have been trying to 
load bioconductor to test compile with the sourceforge g77, but with no 
success over the last week. Something seems to have changed, since I was 
able to get further along before then.

On the Powebook, I do the standard connect to 
http://www.bioconductor.org/getBioC.R and the do the getBioC(). It spins 
for a few seconds, then gives an error message "Error in getBioC()" but 
with no additional diagnostic information. This is the same if I ask for 
default or specific packages. I also tried "verbose = TRUE" and got no 
additional info. When I try on the XServe, I get an error message "Error 
in file(file, "wb") : unable to open connection".

I am sure that I wasn't getting these messages when I first tried 
loading bioconductor to the XServe.

Any idea of what is up?
Thanks
Mike Redmond
UW-Madison
---

        
Byron Ellis wrote: