Dear all:
I am developing my package for my projects, and I have done couple of
utility function that used for parsing bed files in R. My goal is to parse
and analyze multiple bed files in parallel, in ideal case, we have three
sample that comes from chip-seq experiments where each has different
Hi, BioC devel:
I have been working on my packages and it is about to close up works except
FDR estimations. However, I have started to read & load three replicates
(bed file format) in GRanges objects, and I have to consider the case when
chosen sample is Biological or Technical respectively ,so
Bioc-devel:
I haven been developing Bioconductor Package for multiple sample peak
calling, and all unit test for my packages is done efficiently. However, I
have one minor problem that cause memory inefficiency when building the
packages in my machines. To get straight, I am going to find overlap
BiocDevel:
I aware that this question raised in the mailing list weeks ago, and I
followed the thread to possibly fix the problem, but I still can't able to
use devel branch after I installed Bioc 3.4. I tried to remove
BiocInstaller from the the directory and try the solution from same thread,
Dear BiocDevel:
I ran into the issue after installed devel version of R and Bioc 3.4.
Because my packages depends on some packages from CRAN repository, now I
failed to installed paclages from CRAN. I don't have problem when I used
released version of R. Because new packages must coordinate with
Hi BiocDevel:
I got an error when tried to install several packages from Bioconductor
(rtracklayer, SummarizedExperiments), so I removed BiocInstaller and
reinstall again now error is gone. But, I got warning which previously
happened when I failed to install rtracklayer packages. Because this
elaborate your answer please ? Thanks
Best regards :
Jurat
On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> Please respond on the mailing list, so that others in similar situations
> can benefit / contribute.
>
> On 11/11/2016 10:39 AM, Ju
sorry for this simple question. why use R vanilla ? not familiar enough
with this term.
On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 11/11/2016 11:42 AM, Jurat Shayidin wrote:
>
>> I'll keep this in mind. Thanks for reminding
/ contribute.
>
> On 11/11/2016 10:39 AM, Jurat Shayidin wrote:
>
>> Dear Martin :
>>
>> Thanks for your prompt hit . I used to have R release version, so after
>> I installed devel version of R, I removed R released version, while only
>> keep devel version
ith R --vanilla the conclusion is that whatever made it fail was something
> loaded by R but not R --vanilla. If it doesn't work with R --vanilla the
> conclusion is that your problem is elsewhere.
>
> Best,
> Kasper
>
> On Fri, Nov 11, 2016 at 12:09 PM, Jurat Shayidin <ju
epherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Jurat Shayidin <juratb...@gmail.com>
Dear BiocDevel :
I got confused about the message from R CMD BiocCheck, and R CMD check on
my packages. Precisely speaking, R CMD check throws an error that my unit
test is failed, zero warning, 2 notes; instead R CMD BiocCheck complain
with one error that no runnable example found, one warning
s under
> .libPaths() by hand. Furthermore, and that's a mistake we see sometimes
> with contributed packages, the code in your package should always
> treat the *package installation folder* as a read-only folder.
>
> Hope this helps,
>
> H.
>
>
> On 12/01/2016 04:34 PM, Jura
Hi BiocDevel :
I am getting vignette error when I building my packages, and external data
can't be captured by system.file() . I did unit test all function of my
packages, it works fine. When I am going to compile package vignette, test
input bed file can't be detected. However, I used
eave(file, quiet = quiet, encoding = enc) :
> > Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to
> > R Markdown v1.
> > Quitting from lines 60-64 (vignette.Rmd)
> > Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> > subscript
.io/.
>
> Finally, you might want to search the manual of how to create R
> extensions for other details.
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html
>
>
> Best,
> Leo
>
> On Fri, Dec 2, 2016 at 12:11 PM, Jurat Shayidin <juratb...@gmail.com>
&
install the
> package, but the inst directory itself goes away.
>
> If in your package source you have the following structure:
>
> inst/extdata/
> inst/foo.txt
>
> In the installed package you end up with:
>
> extdata/
> foo.txt
>
> HTH
> Dan
>
>
> - Origin
Best regards :
Jurat
On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:
> See below.
>
> - Original Message -
> > From: "Jurat Shayidin" <juratb...@gmail.com>
> > To: "Dan Tenenbaum" <dtene...@fredhutc
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Jurat
> Shayidin <juratb...@gmail.com>
> *Sent:* Wednesday, December 28, 2016 6:58:15 AM
> *To:* bioc-devel@r-project.org
>
Dear BiocDevel, Bioconductor Team :
I've read Bioconductor contribution repository, and new package submission
with full instruction, and make sure I am ready to submit my packages --
MSPC -- to Bioconductor projects. However, my package both succeed with R
CMD check, R CMD BiocCheck without any
stics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Jurat
> Shayidin <juratb...@gmail.com>
> *Sent:* Tuesday, December 20, 2016
s
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Jurat
> Shayidin <juratb...@gmail.com>
> *Sent:* Friday, December 23, 2016 8:29:45 AM
> *To:* bioc-devel@r-project.o
Dear Bioconductor team :
Since I've issued new package submission to Bioconductor project, there is
no update on assigner for my packages. I am sure that I did follow
Bioconductor package submission, and contribution instruction. I believe
evaluating new packages could takes time, but I don't
Dear BiocDevel, Bioconductor team :
I want to know how can I get further assessment and assist for my package
to Bioconductor Project. I've created issue to
https://github.com/Bioconductor/Contributions and system marked as "Review
in Progress", package reviewer was assigned. Since my submission,
of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Jurat
> Shayidin <juratb...@gmail.com>
> *Sent:* Thursday, Dece
d
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Jurat Shayidin <juratb...@gmail.com&g
Hi:
This happened to me several times, and I figured out the issue. I tried to
remove `rtracklayer` package completely from `R` home directory; you can
try: remove.packages("rtracklayer"). Don't be panic, if this problem still
bumps up again, try to reboot your PC (you may need to restart your
27 matches
Mail list logo
