Hi everyone,
Just a reminder - Friday, March 27, 2015 is the deadline for submitting
new
packages. If you submit your package on Friday, your package will still
be considered for the upcoming release.
A detailed release schedule can be found here:
http://bioconductor.org/developers/release-s
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
- Original Message -
> From: "Bernat Gel"
> To: bioc-devel@r-project.org
> Sent: Friday, March 20, 2015 8:06:59 AM
> Subject: [Bioc-devel] Error on Windows when selecting a single chromosome
> from a BSgenome
>
> Hi all,
>
> We are trying to get our first package (regioneR) includ
- Original Message -
> From: "Vladislav Petyuk"
> To: bioc-devel@r-project.org
> Sent: Friday, March 20, 2015 2:43:03 PM
> Subject: [Bioc-devel] Mavericks "Not Supported" message
>
> Hi,
> Could someone tell me about the possible causes of "...NOT
> SUPPORTED...NOT
> SUPPORTED...NOT SUP
Hi,
Could someone tell me about the possible causes of "...NOT SUPPORTED...NOT
SUPPORTED...NOT SUPPORTED..." message for OS X Mavericks?
http://www.bioconductor.org/checkResults/devel/bioc-LATEST/
Mavericks is the OS I developed my package on.
Thank you,
Vlad
[[alternative HTML version del
- Original Message -
> From: "Jianhong Ou"
> To: bioc-devel@r-project.org
> Sent: Thursday, March 19, 2015 8:36:28 AM
> Subject: [Bioc-devel] How to remove warnings when load BiocGenerics,
> AnnotationDbi and GenomeInfoDb
>
> Hi,
>
> How could we mask the warnings when we check a pack
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="/")'
Hi all,
We are trying to get our first package (regioneR) included into
Bioconductor. A couple of months ago it passed all the automatic checks
but now, without code changes from our part fails on windows.
I've been digging and it seems the problem arises when selecting a
single chromosome f
[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
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