Hi Nate,
Thanks a lot for your really quick help, your updated suggestions really
work great! I could not yet take advantage from the new version of
VariantAnnotation, since the changes have not been propagated to the
package archive. It seems that currently many packages are broken,
especial
I've updated the Rsamtools Using samtools C libraries vignette. I've
also updated VariantAnnotation and other packages that link to samtools
libraries. They should be available tomorrow, or you can download the
source from subversion if you're in a hurry.
Before you had for your Makevars (with
On 03/20/2015 06:39 AM, Ulrich Bodenhofer wrote:
> [list admins: please delete my previous incomplete message from the
> list; sorry for any inconvenience]
>
> Hi,
>
> Next update (I am deeply sorry for sending so many replies, but I
> think these might be interesting for users who face the sam
The Makevars.win you say works for Windows is the current recommendation
for Makevars.win in the Rsamtools Using samtools C libraries vignette.
Regarding the Linux issue, yes, the r_arch argument to configure is
adding the intermediate subdirectory. It is my fault the current (Linux)
recommenda
On 03/20/2015 04:50 AM, Ulrich Bodenhofer wrote:
Hi,
Sorry for bothering you with another update on this matter. I changed the
Makevars file to the following:
SAMTOOLS_PATH=\
`echo 'cat(system.file("usrlib", package="Rsamtools",
mustWork=TRUE), .Platform[["r_arch"]], sep="/")'
[list admins: please delete my previous incomplete message from the
list; sorry for any inconvenience]
Hi,
Next update (I am deeply sorry for sending so many replies, but I think
these might be interesting for users who face the same issues): I did
another clean install on Windows and used the
Hi,
Next update (I am deeply sorry for sending so many replies, but I think
these might be interesting for users who face the same issues): I did
another clean install on Windows and used the following Makevars.win
(which I copied from VariantAnnotation):
On 03/19/2015 06:11 PM, Nathaniel Ha
Hi,
Sorry for bothering you with another update on this matter. I changed
the Makevars file to the following:
SAMTOOLS_PATH=\
`echo 'cat(system.file("usrlib", package="Rsamtools",
mustWork=TRUE), .Platform[["r_arch"]], sep="/")' |\
"${R_HOME}/bin/R" --vanilla --slave`
Hi Nate,
Thanks also for this useful hint! I will definitely consider it, but not
immediately. I have seen that the tabix API (which is the only part of
Rsamtools I am using) has changed significantly in Rhtslib as compared
to Rsamtools. So I do not think I will manage to change my code before
Hi Nate,
Thanks for your quick and enlightening reply!
No, I was actually not aware that the suggested code for the Makevars
file has changed. I updated that in my package and the problem persists:
the statement in the Makevars file (also the updated one in the
documentation you suggested) as
Also, please consider developing your package against the new and
improved version of samtools, htslib, available via the Rhtslib package.
The samtools source in Rsamtools will eventually go away in favor of the
htslib library.
See announcement of Rhtslib:
https://stat.ethz.ch/pipermail/bioc-
Hi, Ulrich. I just built R-devel (on Ubuntu) from trunk and installed
Rsamtools using biocLite; the libraries ended up where I expect them:
> dir(system.file(package="Rsamtools", "usrlib"))
[1] "libbam.a" "libbcf.a" "libtabix.a"
> sessionInfo()
R Under development (unstable) (2015-03-19 r6803
Hi,
I am currently finishing a package for submission to Bioconductor 3.1
and, therefore, I am trying to make everything work on the latest
R-devel, but I have an issue with linking to Rsamtools. It seems that
Rsamtools installs the libraries libbam, libbcf, and libtabix to the
usrlib/x86_64/
13 matches
Mail list logo
