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

Wed Nov 18 19:05:12 CET 2015

Just to mark that as solved:

Seems as I've just been at the wrong place on the wrong time (by using
R-devel r69640 downloaded yesterday).

When compiling from the most recent R-devel_2015-11-17_r69648.tar.gz
available from cran, I neither encountered the biocLite problem under
linux nor the gfortran version issue with acepack under Mac OS X El
Capitan.

Thx for helping on that!

Ludwig

> (Sorry for the top-post).
>
> Yes, your R-devel issues on linux are due to Michael's commits. I believe
> this has been addressed, but in the commit r69641; you were building
> against r69640, so one commit too early! I guess you downloaded a tar.gz
> file, and these 'snapshots' are created nightly. For more recent versions
> you'll need either to wait or to use svn, along the lines of
>
> mkdir -p ~/src/; cd ~/src
> svn co https://svn.r-project.org/R/trunk R-devel
> R-devel/tools/rsync-recommended
> mkdir -p ~/bin/R-devel; cd ~/bin/R-devel
> ~/src/R-devel/configure
> make -j
> ________________________________________
> From: Ludwig Geistlinger [Ludwig.Geistlinger at bio.ifi.lmu.de]
> Sent: Wednesday, November 18, 2015 10:14 AM
> To: Morgan, Martin
> Subject: RE: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El
> Capitan 10.11.1
>
> Dear Martin,
>
>>>> it should be possible to use gfortran-5.2 via editing the
>>>> R_HOME/etc/Makeconf or ~/.R/Makevars.
>>>>
>
> I will of course try that - it's not about taking your suggestion lightly,
> just trying out what is working for me.
>
>> 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.
>
> Is this refering to linux issue, I reported? And what is the meaning of
> your suggestions here? Should I wait for Michael Lawrence commits to take
> place?
>
>> 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’
>
>
>
> Thx,
> Ludwig
>
>
>> 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
>> ________________________________________
>> 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 8:46 AM
>> To: bioc-devel at r-project.org
>> Subject: Re: [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 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
>>>>
>>>> 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 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
>>
>> _______________________________________________
>> 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.
>>
>
>
> --
> 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
>
>
> 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.
>