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 f
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,
pr
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 d
efit / 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 ver
d you
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 A
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 remi
with 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 Shay
;
> ----- Original Message -
> > From: "Jurat Shayidin"
> > To: "Kasper Daniel Hansen" , "bioc-devel"
>
> > Sent: Friday, November 11, 2016 12:38:57 PM
> > Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after
> ins
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
war
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 devtools::i
ever try to modify anything that is 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
o git?
>
> Note that everything _under_ inst gets installed when you 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
How I fix R CMD check error above ? system.file() still can't detect
external data. Any idea please ? Thanks a lot
Best regards :
Jurat
On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum
wrote:
> See below.
>
> - Original Message -
> > From: "Jurat Shayidin&qu
n't get as far as you (error in lines 60-64).
>
> As Herve suggests, please run R CMD check from a directory that you have
> write permission in, such as your home directory.
>
> R CMD check will alert you about various problems, including referring to
> packages in NAMESP
data
> git commit
> git push
>
> Dan
>
>
>
> - Original Message -
> > From: "Jurat Shayidin"
> > To: "Dan Tenenbaum" , "bioc-devel" <
> bioc-devel@r-project.org>
> > Sent: Sunday, December 4, 2016 5:12:50 AM
>
://builder.r-hub.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
> wrote:
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 (I
gt; Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel on behalf of Jurat
> Shayidin
> *Sent:* Thursday, December 15, 2016 7:17:42 AM
> *To:* bioc-devel@r-project
t;
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Jurat Shayidin
> *Se
s.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Jurat Shayidin
&
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 e
stics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------
> *From:* Bioc-devel on behalf of Jurat
> Shayidin
> *Sent:* Tuesday, December 20, 2016 6:35:52 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [B
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 have
s
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel on behalf of Jurat
> Shayidin
> *Sent:* Friday, December 23, 2016 8:29:45 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] Question about status of new packag
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,
atics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel on behalf of Jurat
> Shayidin
> *Sent:* Wednesday, December 28, 2016 6:58:15 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] How to get further assessment
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 PC
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
le
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
Dear Mailing list:
I got stuck with implementing wrapper function for my packages. when three
GRanges objects (e.g. a,b,c) are given to my function, I would like to find
overlapped regions from one to another in parallel, where a as query, b,c
are subjects respectively. Because of three input was
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