date:20150208

Re: [Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

2015-02-08 Thread Ulrich Bodenhofer


Hi Hervé,

Thank you for your positive reply and thanks a lot in advance for your 
efforts putting the packages together! Just that you know, I am not 
personally in desperate need for these packages. I am currently 
finishing a GWAS-related package and I thought it would be nice to 
integrate support for the latest human genome build, but I think it is 
not (yet) a must-have feature. I do not know whether there are actually 
hg38-/GRCh38-based VCF files around yet, but I'm sure it is only a 
matter of time until they are.


Thanks and best regards,
Ulrich


On 02/09/2015 08:23 AM, Hervé Pagès wrote:

Hi Ulrich,

I was not sure about how much demand there is for the masked BSgenome
packages in general so I was just waiting for someone to ask. Note that
the masks are typically generated from data available at UCSC so it
sounds that it's time to make BSgenome.Hsapiens.NCBI.hg38 and
BSgenome.Hsapiens.NCBI.hg38.masked available.

I'll prepare the 2 packages in the next couple of weeks and post back
here when they are ready for download.

Cheers,
H.

On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:

Hi,

The latest human genome build GRCh38 has been around in Bioconductor for
some while (package BSgenome.Hsapiens.NCBI.GRCh38). As far as I can
tell, however, there is currently no package that provides easy access
to masked/unmasked regions in the genome (like there is a .masked
version that wraps BSgenome objects into MaskedBSgenome objects for many
other genomes, e.g. there is BSgenome.Hsapiens.UCSC.hg19.masked for
hg19). Here is my question: does anybody have plans to include a
package BSgenome.Hsapiens.NCBI.GRCh38.masked (or under a different name)
into Bioconductor 3.1? At least I could not find anything in the current
development branch.

Thanks and best regards,
Ulrich


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

Re: [Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

2015-02-08 Thread Hervé Pagès


On 02/08/2015 11:23 PM, Hervé Pagès wrote:

Hi Ulrich,

I was not sure about how much demand there is for the masked BSgenome
packages in general so I was just waiting for someone to ask. Note that
the masks are typically generated from data available at UCSC so it
sounds that it's time to make BSgenome.Hsapiens.NCBI.hg38 and
BSgenome.Hsapiens.NCBI.hg38.masked available.


I meant BSgenome.Hsapiens.UCSC.hg38 and 
BSgenome.Hsapiens.UCSC.hg38.masked, sorry.


H.



I'll prepare the 2 packages in the next couple of weeks and post back
here when they are ready for download.

Cheers,
H.

On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:

Hi,

The latest human genome build GRCh38 has been around in Bioconductor for
some while (package BSgenome.Hsapiens.NCBI.GRCh38). As far as I can
tell, however, there is currently no package that provides easy access
to masked/unmasked regions in the genome (like there is a .masked
version that wraps BSgenome objects into MaskedBSgenome objects for many
other genomes, e.g. there is BSgenome.Hsapiens.UCSC.hg19.masked for
hg19). Here is my question: does anybody have plans to include  a
package BSgenome.Hsapiens.NCBI.GRCh38.masked (or under a different name)
into Bioconductor 3.1? At least I could not find anything in the current
development branch.

Thanks and best regards,
Ulrich



*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics

*Johannes Kepler University*
Altenberger Str. 69
4040 Linz, Austria

Tel. +43 732 2468 4526
Fax +43 732 2468 4539
bodenho...@bioinf.jku.at 
http://www.bioinf.jku.at/ 

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




--
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

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

Re: [Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

2015-02-08 Thread Hervé Pagès


Hi Ulrich,

I was not sure about how much demand there is for the masked BSgenome
packages in general so I was just waiting for someone to ask. Note that
the masks are typically generated from data available at UCSC so it
sounds that it's time to make BSgenome.Hsapiens.NCBI.hg38 and
BSgenome.Hsapiens.NCBI.hg38.masked available.

I'll prepare the 2 packages in the next couple of weeks and post back
here when they are ready for download.

Cheers,
H.

On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:

Hi,

The latest human genome build GRCh38 has been around in Bioconductor for
some while (package BSgenome.Hsapiens.NCBI.GRCh38). As far as I can
tell, however, there is currently no package that provides easy access
to masked/unmasked regions in the genome (like there is a .masked
version that wraps BSgenome objects into MaskedBSgenome objects for many
other genomes, e.g. there is BSgenome.Hsapiens.UCSC.hg19.masked for
hg19). Here is my question: does anybody have plans to include  a
package BSgenome.Hsapiens.NCBI.GRCh38.masked (or under a different name)
into Bioconductor 3.1? At least I could not find anything in the current
development branch.

Thanks and best regards,
Ulrich



*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics

*Johannes Kepler University*
Altenberger Str. 69
4040 Linz, Austria

Tel. +43 732 2468 4526
Fax +43 732 2468 4539
bodenho...@bioinf.jku.at 
http://www.bioinf.jku.at/ 

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


--
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

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

Re: [Bioc-devel] Install edgeR

2015-02-08 Thread Martin Morgan


On 02/08/2015 05:31 AM, de...@gmx.de wrote:


Hi everyone,

I am trying to install the edgeR package on Linux Mint 17 Cinnamon 64-bit.

I have installed R the normal way via
sudo apt-get install r-base


Have you also

  sudo apt-get install r-base-dev

? This is needed to install packages from source and as as described at 
http://cran.r-project.org/bin/linux/ubuntu/.




$ R --version
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"


this is unfortunately an old version of R, hence old version of Bioconductor / 
edgeR. Look instead for R version 3.1.2 which should be widely available from an 
appropriate repository, as described at http://cran.r-project.org/bin/linux/ubuntu/.





So then I proceed according to the instructions at
http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
and type:
source("http://bioconductor.org/biocLite.R";)
biocLite("edgeR")

But then I get:

> biocLite("edgeR")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'edgeR'
trying URL
'http://bioconductor.org/packages/2.13/bioc/src/contrib/edgeR_3.4.2.tar.gz'
Content type 'application/x-gzip' length 1126311 bytes (1.1 Mb)
opened URL
==
downloaded 1.1 Mb
* installing *source* package ‘edgeR’ ...
** libs
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c R_levenberg.cpp -o R_levenberg.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c R_one_group.cpp -o R_one_group.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
-c core/interpolator.cpp -o core/interpolator.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3
-pipe  -g  -c core/fmm_spline.c -o core/fmm_spline.o
g++  -shared  -o  edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o
R_cr_adjust.o   R_levenberg.o  R_maximize_interpolant.o  R_one_group.o
R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o
core/glm_one_group.o core/interpolator.o core/fmm_spline.o -llapack -lblas
-lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [edgeR.so] Error 1
ERROR: compilation failed for package ‘edgeR’
* removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/edgeR’
The downloaded source packages are in
‘/tmp/RtmpezIkbL/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘edgeR’ had non-zero exit status
2: installed directory not writable, cannot update packages 'cluster',
  'KernSmooth', 'Matrix', 'mgcv', 'nlme'


Which sudo apt-get install  do I have to perform in order to resolve
the dependencies?

Also: Why do they not write anything on the bioconductor homepage about this
issue? It only states "Depends: R (>= 2.15.0), limma" ... ?


These list R package dependencies, not operating system dependencies. If your R 
installation is complete, then the system dependencies you are missing will be 
satisfied.


Hope that helps,

Martin


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




--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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

[Bioc-devel] Install edgeR

2015-02-08 Thread def87


   Hi everyone,

   I am trying to install the edgeR package on Linux Mint 17 Cinnamon 64-bit.

   I have installed R the normal way via
   sudo apt-get install r-base

   $ R --version
   R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"

   So then I proceed according to the instructions at
   http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
   and type:
   source("http://bioconductor.org/biocLite.R";)
   biocLite("edgeR")

   But then I get:

   > biocLite("edgeR")
   BioC_mirror: http://bioconductor.org
   Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
   Installing package(s) 'edgeR'
   trying URL
   'http://bioconductor.org/packages/2.13/bioc/src/contrib/edgeR_3.4.2.tar.gz'
   Content type 'application/x-gzip' length 1126311 bytes (1.1 Mb)
   opened URL
   ==
   downloaded 1.1 Mb
   * installing *source* package ‘edgeR’ ...
   ** libs
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c R_loess_by_col.cpp -o R_loess_by_col.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c R_cr_adjust.cpp -o R_cr_adjust.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c R_levenberg.cpp -o R_levenberg.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c R_one_group.cpp -o R_one_group.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c R_simple_good_turing.cpp -o R_simple_good_turing.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c core/adj_coxreid.cpp -o core/adj_coxreid.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c core/glm_levenberg.cpp -o core/glm_levenberg.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c core/glm_one_group.cpp -o core/glm_one_group.o
   g++ -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3 -pipe  -g
   -c core/interpolator.cpp -o core/interpolator.o
   gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./core -I.  -fpic  -O3
   -pipe  -g  -c core/fmm_spline.c -o core/fmm_spline.o
   g++  -shared  -o  edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o
   R_cr_adjust.o   R_levenberg.o  R_maximize_interpolant.o  R_one_group.o
   R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o
   core/glm_one_group.o core/interpolator.o core/fmm_spline.o -llapack -lblas
   -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
   /usr/bin/ld: cannot find -llapack
   /usr/bin/ld: cannot find -lblas
   /usr/bin/ld: cannot find -lgfortran
   collect2: error: ld returned 1 exit status
   make: *** [edgeR.so] Error 1
   ERROR: compilation failed for package ‘edgeR’
   * removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/edgeR’
   The downloaded source packages are in
   ‘/tmp/RtmpezIkbL/downloaded_packages’
   Warning messages:
   1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
 installation of package ‘edgeR’ had non-zero exit status
   2: installed directory not writable, cannot update packages 'cluster',
 'KernSmooth', 'Matrix', 'mgcv', 'nlme'


   Which sudo apt-get install  do I have to perform in order to resolve
   the dependencies?

   Also: Why do they not write anything on the bioconductor homepage about this
   issue? It only states "Depends: R (>= 2.15.0), limma" ... ?
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

Re: [Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

Re: [Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

Re: [Bioc-devel] Install edgeR

[Bioc-devel] Install edgeR

5 matches

Site Navigation

Mail list logo

Footer information