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

Wed Nov 18 14:46:05 CET 2015

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!?):

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help
> biocLite()
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!

> sessionInfo()
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

> Dear Ludwig,
>
> I tried to install that package and it compiled nicely on my system with
>> sessionInfo()
> 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
>
>> On 18 Nov 2015, at 12:12, Morgan, Martin <Martin.Morgan at roswellpark.org>
>> wrote:
>>
>> Probably the definitive answer will be the R-SIG-Mac mailing list
>>
>>  https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> perhaps specifically this thread
>>
>>  https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html
>>
>> which points to the R-admin manual and especially
>>
>>  https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X
>>
>> From the discussion (especially the posts by Brian Ripley) it seems like
>> it should be possible to use gfortran-5.2 via editing the
>> R_HOME/etc/Makeconf or ~/.R/Makevars.
>>
>> Martin
>>
>>
>> ________________________________________
>> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Ludwig
>> Geistlinger [Ludwig.Geistlinger at bio.ifi.lmu.de]
>> Sent: Wednesday, November 18, 2015 5:53 AM
>> To: bioc-devel at r-project.org
>> Subject: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El
>> Capitan      10.11.1
>>
>> Hi,
>>
>> I am experiencing troubles installing "Hmisc", especially its dependency
>> "acepack", via
>>
>>> biocLite("acepack")
>>
>> 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 Übersetzung von
>>  C/C++/Fortran benötigt.: ‘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 überprüft
>> ** 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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>
>

-- 
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de