Re: [Bioc-devel] A bioconductor package archive?

2015-11-18 Thread Hervé Pagès 

Hi Gabe,

On 11/18/2015 09:50 AM, Gabe Becker wrote:

Hi all,

Unless I'm missing something, there is no archive of prior source packages
for Bioconductor, in the vein of CRAN's Web Archive.  It has generally been
accepted, I think, that if you need a version of a package - e.g., for
precise reproducibility - you can go to the still-existing release
repository for that Bioc release, or to the svn.

The difficulty arises in determining where in the svn to look when the
old-release repo has a later version of the package. In my switchr package
I take the first commit with the requested version. This is generally
correct, but it isn't always (for example, I recently found it does not
work with IRanges version 1.20.5). Without a rule to automate the search
process that will work generally, the svn repository while  in principle
guaranteeing that a particular previous package can be re-created, does not
provide this in practice.

I know that going backwards and backfilling an archive of previous
Bioconductor package versions is not feasible, but would it be possible to
start populating an archive now moving forward - with the expectation that
they would be preserved indefinitely - to prevent this in the future?
Automated tagging of package releases within the SVN would probably also
work.


I definitely want to add this tagging. I'm planning to do some work in
December to support incremental builds so we'll be able to switch
between "full build/check of everything" mode and "build/check modified
packages + packages that depend on them only" mode. I'll need to have
the SVN tag in the DESCRIPTION file for this. Will add it soon.

I'll let others speak for the bioconductor package archive.

Cheers,
H.



Best,
~G




Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Unexpected behaviour with Assays and Vector classes

2015-11-18 Thread Hervé Pagès 

Developers,

On 11/16/2015 11:39 PM, Hervé Pagès wrote:

Hi Aaron,

On 11/16/2015 09:39 AM, Hervé Pagès wrote:

[...]

Anyway, you convinced me that we should not try to follow too closely
the names model for how we treat metadata columns. If nobody objects,
I'll change the behavior of the various "replaceROWS" methods in the
S4Vectors stack and make sure that they all transfer the metadata
columns from 'value' to 'x'.


This is done in S4Vectors 0.9.9 and IRanges 2.5.6 in devel, and in
S4Vectors 0.8.3 and IRanges 2.4.2 in release.


Just a heads-up that while making these changes to IRanges, I broke
subsetting of DNAStringSet objects (and other XStringSet derivatives).
So please refrain from updating IRanges today. This is now fixed in
IRanges 2.4.3 (release) and 2.5.7 (devel) but the fix won't become
available via biocLite() before tomorrow.

Sorry for the inconvenience,

H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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[Bioc-devel] A bioconductor package archive?

2015-11-18 Thread Gabe Becker 
Hi all,

Unless I'm missing something, there is no archive of prior source packages
for Bioconductor, in the vein of CRAN's Web Archive.  It has generally been
accepted, I think, that if you need a version of a package - e.g., for
precise reproducibility - you can go to the still-existing release
repository for that Bioc release, or to the svn.

The difficulty arises in determining where in the svn to look when the
old-release repo has a later version of the package. In my switchr package
I take the first commit with the requested version. This is generally
correct, but it isn't always (for example, I recently found it does not
work with IRanges version 1.20.5). Without a rule to automate the search
process that will work generally, the svn repository while  in principle
guaranteeing that a particular previous package can be re-created, does not
provide this in practice.

I know that going backwards and backfilling an archive of previous
Bioconductor package versions is not feasible, but would it be possible to
start populating an archive now moving forward - with the expectation that
they would be preserved indefinitely - to prevent this in the future?
Automated tagging of package releases within the SVN would probably also
work.

Best,
~G




Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

[[alternative HTML version deleted]]

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

2015-11-18 Thread Ludwig Geistlinger 
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

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

2015-11-18 Thread 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!?):

> 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-8LC_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

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

2015-11-18 Thread Morgan, Martin 
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-boun...@r-project.org] on behalf of Ludwig 
Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de]
Sent: Wednesday, November 18, 2015 8:46 AM
To: bioc-devel@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-8LC_MESSAGES=en_US.UTF-8
 [7]

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

2015-11-18 Thread 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.geistlin...@bio.ifi.lmu.de> wrote:

> 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-8LC_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

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

2015-11-18 Thread Rainer Johannes 
Could be that gcc via homebrew takes a while… especially if it is compiling 
that stuff from source…


> On 18 Nov 2015, at 14:46, Ludwig Geistlinger 
>  wrote:
> 
> 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-8LC_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