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

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 ?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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> This email message may contain legally privileged and/or confidential
>> information.  If you are not the intended recipient(s), or the employee
>> or agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited.  If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


--
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit f?r Bioinformatik
Institut f?r Informatik
Ludwig-Maximilians-Universit?t M?nchen
Amalienstrasse 17, 2. Stock, B?ro A201
80333 M?nchen

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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.