Dear Bioconductor,
We are deprecating part of a package. I am following the guidelines in
the "Function Deprecation Guidelines" page at bioconductor.org and I
have a few questions:
(i) Deprecating a S4 method which has the same name in another S4 class.
We have two DelayedArray backends. Fun
Dear Bioconductor,
With your very helpful assistance, for which we are extremely grateful,
we have succeeded in removing the errors from the devel branch of our
bumphunter package. More or less, anyway.
We are passing on celaya2 and failing on merida2. The reason is that
celaya2 is running R
Dear Bioconductor,
Our bumphunter package is failing its unit tests fairly spectacularly:
the pval algorithm seems to be returning a data frame full of zeroes.
Unfortunately, I have not been able to reproduce this behavior. I have
instantiated an EC2 instance with the devel AMI, updated all th
from
> /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:17,
> So could it be an issue with the configure script?
>
> On Mon, Mar 25, 2019 at 7:22 AM Samuela Pollack
> mailto:spoll...@jimmy.harvard.edu>> wrote:
>
> Dear Biocon
hese
changes to the release and devel branches of RBGL? I've given you
permissions... Martin
On 3/22/19, 5:15 AM, "Samuela Pollack" wrote:
We have a temporary fix which we believe will alleviate the difficulty.
The only routine in RBGL that does not compile und
Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> --------
> *From:* Bioc-devel on behalf of
> Samuela Pollack
> *Sent:* Wednesday, February 13, 2019 10:00:18 AM
> *To:* Rafael Irizarry; Leonardo Colla
Dear Bioconductor,
The GenomeInfoDb package is generating an error in 3.8 and causing our
package bumphunter to crash too.
Our test calls GenomeInfoDb::fetchExtendedChromInfoDb and crashes with
an error that says some UCSC seqlevels in hg38 couldn't be mapped to
NCBI seqlevels. The release v
not, then this
is not an issue. If you do choose to follow through with RELEASE_3_8 as well,
please reply to this thread when you have made the de-duplication changes and
added the branch to your GitHub repository.
Best regards,
Nitesh
On Nov 2, 2018, at 5:09 PM, Samuela Pollack wrote:
Dear
Dear Bioconductor,
I believe I have removed all duplicate commits from the bumphunter
package. The main branch in rafalab/bumphunter incorporates the new
commit history. It passes 'library(devtools); build("."); install();
check("."); BiocCheck(".")'
I am contacting you in accordance with it
