Re: [Bioc-devel] Error loading rtracklayer

[Jurat Shayidin]

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
several times), I am sure this could help you out. Cheers :)

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Re: [Bioc-devel] How to get further assessment for newly submitted package?

[Jurat Shayidin]

Dear Lori :

I still didn't get any updated action from reviewer on our packages. We've
planned to complete package submission process by fixing possible issue
raised from Bioconductor team and proceed publication accordingly.we only
need brief, general evaluation on this package and make sure we can able to
do publication. Any chance to speed up package review process please ?
Thank you

Best regards :
Jurat

On Wed, Dec 28, 2016 at 1:43 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

>
> You will receive feedback soon.  Reviewers are assigned multiple packages
> and will review them in the order they were received.  There is also a
> delay because of the holidays season.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department 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:* Wednesday, December 28, 2016 6:58:15 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] How to get further assessment for newly submitted
> package?
>
> 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
> <https://github.com/Bioconductor/Contributions>
> GitHub - Bioconductor/Contributions: Contribute Packages ...
> <https://github.com/Bioconductor/Contributions>
> github.com
> README.md Table of Contents. Contributing a Bioconductor Package; Starting
> the Submission Process; What to Expect; Adding a Web Hook; Submitting
> Related Packages
>
>
> in Progress", package reviewer was assigned. Since my submission, review
> status still  is not updated, haven't receive any update message both from
> system and reviewers. I doubt that's because of holiday session, reviewers
> haven't ready for fresh evaluation. I believe Bioconductor packages
> submission is lengthy process, so I am eager to optimize my packages to
> make acceptance by Bioconductor project, getting brief assessment on my
> package is needed. Any chance to get further evaluation on my packages that
> I possibly work on during this holiday ? Thanks a lot
>
> Best regards :
> --
> Jurat Shahidin
>
> Dipartimento di Elettronica, Informazione e Bioingegneria
> Politecnico di Milano
> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
> Mobile : +39 3279366608 <+39%20327%20936%206608>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> Bioc-devel -- Bioconductor Developers' List - Homepage - SfS
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> stat.ethz.ch
> The Developers' List for the Bioconductor project. Used for release and
> development issues related to release. To see the collection of prior
> postings to the list ...
>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.




-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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[Bioc-devel] How to get further assessment for newly submitted package?

[Jurat Shayidin]

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, review
status still  is not updated, haven't receive any update message both from
system and reviewers. I doubt that's because of holiday session, reviewers
haven't ready for fresh evaluation. I believe Bioconductor packages
submission is lengthy process, so I am eager to optimize my packages to
make acceptance by Bioconductor project, getting brief assessment on my
package is needed. Any chance to get further evaluation on my packages that
I possibly work on during this holiday ? Thanks a lot

Best regards :
-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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Re: [Bioc-devel] Question about status of new package submission

[Jurat Shayidin]

Dear Lori :

Thanks for giving prompt help on this issue. Because of I forked old
version of contribution repository, my package issued on wrong place. Now I
update package submission issue to the suggested repository, it can be
visible the issue list. Thank you very much.

Best regards :

Jurat

On Fri, Dec 23, 2016 at 2:38 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Are you sure you submitted the package to the right location?  Normally we
> see new packages as issues on https://github.com/
> Bioconductor/Contributions/issues once they are submitted. Please ensure
> you use this link to submit your package:  https://github.com/
> Bioconductor/Contributions/issues/new
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department 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:* Friday, December 23, 2016 8:29:45 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] Question about status of new package submission
>
> 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 any update who
> is assigned to review my package. I doubt because of Christmas is
> approaching and there might have some delay for package review. How can I
> make sure that my package submission is under evaluation ? I am ready to
> commit further improvement on my package's implementation based on
> evaluation review from Bioconductor team. Thanks a lot
>
> Best regards :
>
> Jurat
>
> --
> Jurat Shahidin
>
> Dipartimento di Elettronica, Informazione e Bioingegneria
> Politecnico di Milano
> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
> Mobile : +39 3279366608 <+39%20327%20936%206608>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.




-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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[Bioc-devel] Question about status of new package submission

[Jurat Shayidin]

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 any update who
is assigned to review my package. I doubt because of Christmas is
approaching and there might have some delay for package review. How can I
make sure that my package submission is under evaluation ? I am ready to
commit further improvement on my package's implementation based on
evaluation review from Bioconductor team. Thanks a lot

Best regards :

Jurat

-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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Re: [Bioc-devel] New Package submission request to Bioconductor Project

[Jurat Shayidin]

Dear Lori :

Thanks for your prompt response. Yes, I did follow new package submission
guideline from Bioconductor site, package contribution page helped me how
to create new issue, Now I opened the issue for new package submission.
Thanks again for Bioconductor team on kind evaluation of my packages.

Best regards :

Jurat

On Tue, Dec 20, 2016 at 1:01 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> We Thank you for taking the time and diligence to try and have a clean R
> CMD check and BiocCheck before submission.  If these are your only issues
> and you feel the package is ready to be reviewed please submit
> http://bioconductor.org/developers/package-submission/  and your assigned
> reviewer can assist you further.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department 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:* Tuesday, December 20, 2016 6:35:52 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] New Package submission request to Bioconductor
> Project
>
> 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 error, warning. However, R CMD
> BiocCheck alarmed me 2 NOTES about indentation issue on my code, and adding
> NEWS file. I did add NEWS files where specify list of function in current
> version of MSPC packages, but R CMD BiocCheck always gave me same NOTE.
> Plus, I fixed code indentation with 4 space tab, but R CMD BiocCheck still
> alarmed me that 3% of code needs to re-indent. May be Bioconductor team
> guide me how to fix this small issue. To be short, I'll open issue on my
> project repository if this mail is sufficient to inform my request. Thanks
> a lot.
>
> Best regards :
>
> Jurat
>
> --
> Jurat Shahidin
>
> Dipartimento di Elettronica, Informazione e Bioingegneria
> Politecnico di Milano
> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
> Mobile : +39 3279366608 <+39%20327%20936%206608> <+39%20327%20936%206608>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.




-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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[Bioc-devel] New Package submission request to Bioconductor Project

[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 error, warning. However, R CMD
BiocCheck alarmed me 2 NOTES about indentation issue on my code, and adding
NEWS file. I did add NEWS files where specify list of function in current
version of MSPC packages, but R CMD BiocCheck always gave me same NOTE.
Plus, I fixed code indentation with 4 space tab, but R CMD BiocCheck still
alarmed me that 3% of code needs to re-indent. May be Bioconductor team
guide me how to fix this small issue. To be short, I'll open issue on my
project repository if this mail is sufficient to inform my request. Thanks
a lot.

Best regards :

Jurat

-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

[Jurat Shayidin]

Dear Lori :

Thanks for this useful link. I tried dplyr underscore command  separate_,
mutate_ in my implementation,but I got vignette error as follows :

vignette.Rmd' failed with diagnostics: object 'cn' not found. Execution
halted

So I tried another approach that suggested in stackoverflow, I used
utils::globalVariables() at the end of my function :

utils::globalVariables (c ("cn", "p.value", ".", "peakStringency",
"original_list", "n", "Replicate","output"))

but now I got building error as follows:

Error: processing vignette 'MSPC-User-Guide.Rmd' failed with diagnostics:
The namespace for package "MSPC" is locked; no changes in the global
variables list may be made.
Execution halted



I don't know what to do on this R CMD check NOTE. Could you give me
possible solution on this problem ? How can I avoid this issue ? Any
further solution please ? Thank you very much.

Best regards :

Jurat

On Fri, Dec 16, 2016 at 3:15 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> This might be a helpful link
>
> https://cran.r-project.org/web/packages/dplyr/vignettes/nse.html
> Standard Evaluation vs. Non-Standard Evaluation
> <https://cran.r-project.org/web/packages/dplyr/vignettes/nse.html>
> cran.r-project.org
> Standard evaluation basics. Every function in dplyr that uses NSE also has
> a version that uses SE. The name of the SE version is always the NSE name
> with an _ on the end.
>
> and also see the help page in R:   ?globalVariables
>
>
>
> I would ignore the Rmarkdown warning for now if your output is getting
> created correctly and it does not appear in the other checks.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Jurat Shayidin <juratb...@gmail.com>
> *Sent:* Friday, December 16, 2016 8:51:43 AM
>
> *To:* Shepherd, Lori; bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] Quick question about result of R CMD check
> and R CMD BiocCheck
>
> Dear Lori :
>
> Thanks again for your prompt respond. I corrected my mistake, now
> Reference can be printed out. However, R CMD check raised one NOTE, how can
> I fix this ? I've searched related question in stackoverflow and tried
> given solution, but it cause error instead. How can I possibly get rid of
> this NOTE ? Could you give me idea to address this problem please?
>
> Plus, R markdown report warnings but that doesn't effect output of package
> vignette, even R CMD check, and R CMD BiocCheck didn't report this as a
> warning . Should I ignore this ? Thank you very much
>
> Best regards :
> Jurat
>
> On Fri, Dec 16, 2016 at 2:09 PM, Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
>>
>> You should change the references in your vignette MSPC-User-Guide.Rmd not
>> in the bibliography.bib file.  In your vignette, use the tag not the title;
>> so as an example:
>>
>>  [@ Using combined evidence from replicates to evaluate ChIP-seq peaks.]
>>
>> would become [@Vahid_Jalili_MSPC_2015]
>>
>>
>>
>> Once you submit your package to Bioconductor, a reviewer will be assigned
>> to formally review your package and advise on additional changes.
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> --
>> *From:* Jurat Shayidin <juratb...@gmail.com>
>> *Sent:* Friday, December 16, 2016 6:06:41 AM
>> *To:* Shepherd, Lori; bioc-devel@r-project.org
>> *Subject:* Re: [Bioc-devel] Quick question about result of R CMD check
>> and R CMD BiocCheck
>>
>> Dear Lori:
>>
>> Thanks for your respond on my question. I fixed the error from unit test.
>> I tried to edit the tag on bibliography.bib file, but Rstudio still did not
>> print that out. Why is that?
>>
>> R CMD check report only one Notes when I tried to generate stack bar plot
>> for my output set by using ggplot2 packages, this note also appeared in R
>> CMD BiocCheck. I really don't know how to get rid of this note. Any idea
>> please ? How to remove this note ? Should I suppress this? Here is note
>> that raised by R CMD check :
>>
>> Undefined global functions or variables:
>>   . Replicate cn mcols<- n original_list output p.value peakStringency
>>
>&g

Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

[Jurat Shayidin]

Dear Lori :

Thanks again for your prompt respond. I corrected my mistake, now Reference
can be printed out. However, R CMD check raised one NOTE, how can I fix
this ? I've searched related question in stackoverflow and tried given
solution, but it cause error instead. How can I possibly get rid of this
NOTE ? Could you give me idea to address this problem please?

Plus, R markdown report warnings but that doesn't effect output of package
vignette, even R CMD check, and R CMD BiocCheck didn't report this as a
warning . Should I ignore this ? Thank you very much

Best regards :
Jurat

On Fri, Dec 16, 2016 at 2:09 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

>
> You should change the references in your vignette MSPC-User-Guide.Rmd not
> in the bibliography.bib file.  In your vignette, use the tag not the title;
> so as an example:
>
>  [@ Using combined evidence from replicates to evaluate ChIP-seq peaks.]
>
> would become [@Vahid_Jalili_MSPC_2015]
>
>
>
> Once you submit your package to Bioconductor, a reviewer will be assigned
> to formally review your package and advise on additional changes.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Jurat Shayidin <juratb...@gmail.com>
> *Sent:* Friday, December 16, 2016 6:06:41 AM
> *To:* Shepherd, Lori; bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] Quick question about result of R CMD check
> and R CMD BiocCheck
>
> Dear Lori:
>
> Thanks for your respond on my question. I fixed the error from unit test.
> I tried to edit the tag on bibliography.bib file, but Rstudio still did not
> print that out. Why is that?
>
> R CMD check report only one Notes when I tried to generate stack bar plot
> for my output set by using ggplot2 packages, this note also appeared in R
> CMD BiocCheck. I really don't know how to get rid of this note. Any idea
> please ? How to remove this note ? Should I suppress this? Here is note
> that raised by R CMD check :
>
> Undefined global functions or variables:
>   . Replicate cn mcols<- n original_list output p.value peakStringency
>
> plus, I've used tidyr package to categorize my intermediate output in
> order to get desired result, but when I execute .Rmd files, it gaves
> warning, that didn't appeared in R CMD check, R CMD BiocCheck. Because R
> CMD check, R CMD BiocCheck never report this as a warning. Should I keep
> aside this ? R markdown report this warning :
>
> Warning messages:
> 1: Too many values at 158 locations: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
> 12, 13, 14, 15, 16, 17, 18, 19, 20, ...
>
>
> What possible changes I might to do on my package before issuing package
> submission? Thank you very much.
>
> Best regards :
>
> Jurat
>
>
>
> On Thu, Dec 15, 2016 at 2:36 PM, Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
>> $error
>> [1] "At least 80% of man pages documenting exported objects must have
>> runnable examples. The following pages do not:"
>>
>> This ERROR occurs when man pages are included without runnable examples.
>> You have examples in it looks like 5/12 of your man pages (~42%). We
>> encourage 80%
>>
>> $warning
>> [1] "Add non-empty \\value sections to the following man pages:
>> man/filterBycombStringency.Rd"
>>
>> Most man pages encourage a \value{} section describing the output of the
>> function or what would be returned.  This is asking that you add this
>> section to this specific man page with information about what the function
>> returns.
>>
>>
>> On quick glance I think you would cite the references in the bibliography
>> with the tag
>> Vahid_Jalili_MSPC_2015  not the title "Using combined evidence from
>> replicates to evaluate ChIP-seq peaks"
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department 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, December 15, 2016 7:17:42 AM
>> *To:* bioc-devel@r-project.org
>> *Subject:* [Bioc-devel] Quick question about result of R CMD check and R
>> CMD BiocCheck
>>
>> Dear BiocDevel :
>>
>> I got confused about the message fro

Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

[Jurat Shayidin]

Dear Lori:

Thanks for your respond on my question. I fixed the error from unit test. I
tried to edit the tag on bibliography.bib file, but Rstudio still did not
print that out. Why is that?

R CMD check report only one Notes when I tried to generate stack bar plot
for my output set by using ggplot2 packages, this note also appeared in R
CMD BiocCheck. I really don't know how to get rid of this note. Any idea
please ? How to remove this note ? Should I suppress this? Here is note
that raised by R CMD check :

Undefined global functions or variables:
  . Replicate cn mcols<- n original_list output p.value peakStringency

plus, I've used tidyr package to categorize my intermediate output in order
to get desired result, but when I execute .Rmd files, it gaves warning,
that didn't appeared in R CMD check, R CMD BiocCheck. Because R CMD check,
R CMD BiocCheck never report this as a warning. Should I keep aside this ?
R markdown report this warning :

Warning messages:
1: Too many values at 158 locations: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, ...


What possible changes I might to do on my package before issuing package
submission? Thank you very much.

Best regards :

Jurat



On Thu, Dec 15, 2016 at 2:36 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> $error
> [1] "At least 80% of man pages documenting exported objects must have
> runnable examples. The following pages do not:"
>
> This ERROR occurs when man pages are included without runnable examples.
> You have examples in it looks like 5/12 of your man pages (~42%). We
> encourage 80%
>
> $warning
> [1] "Add non-empty \\value sections to the following man pages:
> man/filterBycombStringency.Rd"
>
> Most man pages encourage a \value{} section describing the output of the
> function or what would be returned.  This is asking that you add this
> section to this specific man page with information about what the function
> returns.
>
>
> On quick glance I think you would cite the references in the bibliography
> with the tag
> Vahid_Jalili_MSPC_2015  not the title "Using combined evidence from
> replicates to evaluate ChIP-seq peaks"
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department 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, December 15, 2016 7:17:42 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] Quick question about result of R CMD check and R
> CMD BiocCheck
>
> 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 don't
> undersand this warning, becuase R CMD check doesn't report this), 4 notes.
> I don't understand the result of R CMD BiocCheck, can't figure out the
> exact issue . However, result of R CMD check is more clear and
> self-explanatory. I did add example for each of my function, R CMD check
> okay with it, but R CMD BiocCheck complain about this, Why ? How to address
> the issues raised by R CMD BiocCheck ?  R CMD BiocCheck gave me following
> message :
>
> $error
> [1] "At least 80% of man pages documenting exported objects must have
> runnable examples. The following pages do not:"
>
> $warning
> [1] "Add non-empty \\value sections to the following man pages:
> man/filterBycombStringency.Rd"
>
>
>
> Plus, I tried to attach bibliography.bib files on my package's vignette,
> but Rstudio didn't print out the bibliography information at the end of
> .Rmd file. How can I make this happen ? I did push all recent changes to
> github <https://github.com/julaiti/MSPC>, so everything is synchronized.
> Is
> that possible to kindly ask Bioconductor team to briefly review my packages
> and getting valuable opinion to improve my work? I am grad students and
> very few experiences in Bioinformatics field (not in this major), so my
> very first R package might have a lot of issues, getting possible
> contribution would be highly appreciated. Many thanks to Bioconductor team.
>
> Best regards :
>
> --
> Jurat Shahidin
>
> Dipartimento di Elettronica, Informazione e Bioingegneria
> Politecnico di Milano
> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
> Mobile : +39 3279366608 <+39%20327%20936%206608> <+39%20327%20936%206608>

[Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

[Jurat Shayidin]

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 don't
undersand this warning, becuase R CMD check doesn't report this), 4 notes.
I don't understand the result of R CMD BiocCheck, can't figure out the
exact issue . However, result of R CMD check is more clear and
self-explanatory. I did add example for each of my function, R CMD check
okay with it, but R CMD BiocCheck complain about this, Why ? How to address
the issues raised by R CMD BiocCheck ?  R CMD BiocCheck gave me following
message :

$error
[1] "At least 80% of man pages documenting exported objects must have
runnable examples. The following pages do not:"

$warning
[1] "Add non-empty \\value sections to the following man pages:
man/filterBycombStringency.Rd"



Plus, I tried to attach bibliography.bib files on my package's vignette,
but Rstudio didn't print out the bibliography information at the end of
.Rmd file. How can I make this happen ? I did push all recent changes to
github , so everything is synchronized. Is
that possible to kindly ask Bioconductor team to briefly review my packages
and getting valuable opinion to improve my work? I am grad students and
very few experiences in Bioinformatics field (not in this major), so my
very first R package might have a lot of issues, getting possible
contribution would be highly appreciated. Many thanks to Bioconductor team.

Best regards :

-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Jurat Shayidin]

Dear Leonardo :

Thanks again for your helpful package to resolve my doubt. Through Dan's
kind instruction, previous problems are partially solved instead still
getting error with vignette compilation. I reproduced example bed files and
tried most simplest way to load these data to let vignette compilation
work, but it returned empty list again. In my vignette, line-45 to line-65
gives me error, so I come up with dummy example  line-71 to line-82 to let
data available for my workflow, but still no luck with that. Could you give
me possible help on this issue please ? Here is where my package hosted on
github: https://github.com/julaiti/MSPC

I pushed all my changes to github, so everything is synchronized both in
local machine and github. However, I used data set from Encode consortium
for whole my development (I did add these bed files on github), and using
this bed file to test all my workflow is fine. Because Encode samples are
rather big (about 150MB), I am not sure putting these data set on github
under inst\extdata directory or not. Should I available these big bed files
to my packages ? I checked your packages, and there is no such big files. I
am sorry if my question is naive to ask here.

Plus, R CMD check alarmed me several issues that needed to be solved, Could
you give me possible idea how to overcome this problem ? How to make
initial vignette compilation smooth ? Thank you very much

Best regards :

Jurat

On Fri, Dec 2, 2016 at 6:26 PM, Leonardo Collado Torres <lcoll...@jhu.edu>
wrote:

> Dear Jurat,
>
> Maybe it'll be helpful to you if you see how other packages have their
> data. For example, take a look at one of my packages:
> https://github.com/lcolladotor/derfinder
>
> You'll see that I have two directories inside /inst/extdata with some
> files that I use in my vignette code. See
> https://github.com/lcolladotor/derfinder/tree/master/inst/extdata for
> the files and search system.file() inside
> https://github.com/lcolladotor/derfinder/blob/master/vignettes/derfinder-
> quickstart.Rmd
> to see how I use it in the vignette.
>
> Regarding your permissions issue, I don't recall right now how to get
> this to work with Windows. But basically you can see that error at:
>
> Warning in dir.create(pkgoutdir, mode = "0755") :
>   cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
> reason 'Permission denied'
>
>
> Is your user in your windows machine part of the "administrators"
> group? If not, that could be why. You could otherwise run R CMD build
> and upload your tar ball (a .tar.gz file) to
> https://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 <juratb...@gmail.com>
> wrote:
> > Dear Dan :
> >
> > I forgot to commit vignette file,  now I pushed new changes, so now error
> > could be something else. People in stackoverflow suggest me to put all my
> > external data (a.k.a, bed files) into vignette folder, try to run R CMD
> > check and see what happen, I did this solution, but it doesn't work.
> Plus,
> > I checked file permission of my package parent directory, seems fine to
> me.
> > How I check file permission of my package ?
> > How can I fix this write permission on my machine ? This is not intuitive
> > to me, Any hint please ?
> >
> > Herve suggest me don't create inst/extdata directory manually, but I
> still
> > can't let external data available for vignette code. FYI, my objective in
> > vignette file : let external data available for package use, compile
> > trivial version of vignette with no error, then continue to make it
> > perfect.  Here is updated session of R CMD check :
> >
> >
> > Microsoft Windows [Version 6.3.9600]
> > (c) 2013 Microsoft Corporation. All rights reserved.
> >
> > C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
> >
> > C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
> > "C:\Users\jvrat\Documents\MSPC"
> > * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
> > * installing *source* package 'MSPC' ...
> > ** R
> > ** inst
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** installing vignettes
> > ** testing if installed package can be loaded
> > * DONE (MSPC)
> >
> > C:\Program Files\R\R-devel\bin\x64>R CMD check
> > "C:\Users\jvrat\Documents\MSPC"
> > Warning in dir.create(pkgoutdir, mode = "0755") :
&g

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Jurat Shayidin]

Dear Dan :

Thanks again for your kind help. I did clean up my package git working
tree, make every commit readable, tractable. I've read about R writing
extension manual and that helped a lot. Many thanks to Herve' insightful
answer to overcome file permission issue, R CMD check working perfectly
now. Through the long list of R CMD check report, CMD check alarmed me
several possible issues on my packages, and I am working on it.  Plus, R
CMD check complained about some hidden file such as .gitignore,
.Rproj.user, .git . Therefore I did strip away these files following this
way :


C:\Windows\system32>cd C:\Program Files\R\R-devel\bin\x64

C:\Program Files\R\R-devel\bin\x64>R CMD build
"C:\Users\jvrat\Documents\MSPC"
* checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
* preparing 'MSPC':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory 'MSPC/tests/testthat'
* building 'MSPC_0.99.0.tar.gz'


C:\Program Files\R\R-devel\bin\x64>R CMD check "MSPC_0.99.0.tar.gz"
* using log directory 'C:/Program Files/R/R-devel/bin/x64/MSPC.Rcheck'
* using R Under development (unstable) (2016-11-09 r71642)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'MSPC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSPC' version '0.99.0'
* checking package namespace information ... OK

Now inst/ directory is created in MSPC_0.99.0.tar.gz, I could add my
external data in extdata (I think I need manually create extdata folder)
and make available these data for vignette code. But How can I commit these
changes to git automatically ? Because MSPC_0.99.0.tar.gz was not in my
package directory, I cannot push these changes to git. Could you give me
possible idea please ? Many thanks to Bioconductor Project team.

Best regards :
Jurat

On Fri, Dec 2, 2016 at 7:05 PM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:

> I tried building your package, there are a number of issues with it.
>
> I recommend that you 1) always be aware of what is and is not in github,
> by using the 'git status' command. Bear in mind that if files are not
> committed to git then we will not be able to see them and not be able to
> help you. Specifically, the inst folder and everything under it does not
> exist in the github repository. Therefore I get an error in the chunk at
> lines 45-50, I don'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 NAMESPACE but not DESCRIPTION, relying on BiocStyle but not
> mentioning it in DESCRIPTION, etc.
>
> Dan
>
>
>
> - Original Message -
> > From: "Jurat Shayidin" <juratb...@gmail.com>
> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
> bioc-devel@r-project.org>
> > Sent: Friday, December 2, 2016 9:11:29 AM
> > Subject: Re: [Bioc-devel] package vignette error : external data can't
> be captured when compiling package vignette
>
> > Dear Dan :
> >
> > I forgot to commit vignette file,  now I pushed new changes, so now error
> > could be something else. People in stackoverflow suggest me to put all my
> > external data (a.k.a, bed files) into vignette folder, try to run R CMD
> > check and see what happen, I did this solution, but it doesn't work.
> Plus,
> > I checked file permission of my package parent directory, seems fine to
> me.
> > How I check file permission of my package ?
> > How can I fix this write permission on my machine ? This is not intuitive
> > to me, Any hint please ?
> >
> > Herve suggest me don't create inst/extdata directory manually, but I
> still
> > can't let external data available for vignette code. FYI, my objective in
> > vignette file : let external data available for package use, compile
> > trivial version of vignette with no error, then continue to make it
> > perfect.  Here is updated session of R CMD check :
> >
> >
> > Microsoft Windows [Version 6.3.9600]
> > (c) 2013 Microsoft Corporation. All rights reserved.
> >
> > C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
> >
> > C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
> > "C:\Users\jvrat\Documents\MSPC"
> > * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
> > * installing *source* package 'MSPC' ...
> > ** R
> > ** inst
>

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Jurat Shayidin]

Dear Dan :

I forgot to commit vignette file,  now I pushed new changes, so now error
could be something else. People in stackoverflow suggest me to put all my
external data (a.k.a, bed files) into vignette folder, try to run R CMD
check and see what happen, I did this solution, but it doesn't work. Plus,
I checked file permission of my package parent directory, seems fine to me.
How I check file permission of my package ?
How can I fix this write permission on my machine ? This is not intuitive
to me, Any hint please ?

Herve suggest me don't create inst/extdata directory manually, but I still
can't let external data available for vignette code. FYI, my objective in
vignette file : let external data available for package use, compile
trivial version of vignette with no error, then continue to make it
perfect.  Here is updated session of R CMD check :


Microsoft Windows [Version 6.3.9600]
(c) 2013 Microsoft Corporation. All rights reserved.

C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64

C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
"C:\Users\jvrat\Documents\MSPC"
* installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
* installing *source* package 'MSPC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSPC)

C:\Program Files\R\R-devel\bin\x64>R CMD check
"C:\Users\jvrat\Documents\MSPC"
Warning in dir.create(pkgoutdir, mode = "0755") :
  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
reason 'Permission denied'
ERROR: cannot create check dir 'C:/Program
Files/R/R-devel/bin/x64/MSPC.Rcheck'

C:\Program Files\R\R-devel\bin\x64>R CMD build
"C:\Users\jvrat\Documents\MSPC"
* checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
* preparing 'MSPC':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command
'"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages= -e
"tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Warning in engine$weave(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 out of bounds
Execution halted

C:\Program Files\R\R-devel\bin\x64>


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 <dtene...@fredhutch.org>
wrote:

> See below.
>
> - Original Message -
> > From: "Jurat Shayidin" <juratb...@gmail.com>
> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
> bioc-devel@r-project.org>
> > Sent: Friday, December 2, 2016 8:32:35 AM
> > Subject: Re: [Bioc-devel] package vignette error : external data can't
> be captured when compiling package vignette
>
> > Dear Dan :
> >
> > Really appreciated for your quick respond. Instead, I am using R CMD
> check
> > on my packages, I have an error. Here is whole session detail :
> >
> > Microsoft Windows [Version 6.3.9600]
> > (c) 2013 Microsoft Corporation. All rights reserved.
> >
> > C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
> >
> > C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
> > "C:\Users\jvrat\Documents\MSPC"
> > * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
> > * installing *source* package 'MSPC' ...
> > ** R
> > ** inst
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** installing vignettes
> > ** testing if installed package can be loaded
> > * DONE (MSPC)
> >
> > C:\Program Files\R\R-devel\bin\x64>R CMD check
> > "C:\Users\jvrat\Documents\MSPC"
> > Warning in dir.create(pkgoutdir, mode = "0755") :
> >  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
> reason
> > 'Permission denied'
> > ERROR: cannot create check dir 'C:/Program
> > Files/R/R-devel/bin/x64/MSPC.Rcheck'
>
> You need to run R CMD check in a directory where you have write
> permissions.
>
>
> >
> > C:\Program Files\R\R-devel\bin\x64>R CMD build
> > "C:\Users\jvrat\Documents\MSPC"
> > * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
> > * preparing 'MSPC':
> > * checking DESCRIPTION meta-information ... 

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Jurat Shayidin]

Dear Dan :

Really appreciated for your quick respond. Instead, I am using R CMD check
on my packages, I have an error. Here is whole session detail :

Microsoft Windows [Version 6.3.9600]
(c) 2013 Microsoft Corporation. All rights reserved.

C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64

C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
"C:\Users\jvrat\Documents\MSPC"
* installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
* installing *source* package 'MSPC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSPC)

C:\Program Files\R\R-devel\bin\x64>R CMD check
"C:\Users\jvrat\Documents\MSPC"
Warning in dir.create(pkgoutdir, mode = "0755") :
  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck', reason
'Permission denied'
ERROR: cannot create check dir 'C:/Program
Files/R/R-devel/bin/x64/MSPC.Rcheck'

C:\Program Files\R\R-devel\bin\x64>R CMD build
"C:\Users\jvrat\Documents\MSPC"
* checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
* preparing 'MSPC':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command
'"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages= -e
"tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to
R Markdown v1.
Quitting from lines 62-66 (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
object 'inputData' not found
Execution halted

C:\Program Files\R\R-devel\bin\x64>


How can I fix this R CMD check error ? Instead people in stackoverflow
remind me that using devtools packages is not stable some times, so I go
for old fashion : use CMD. Plus, still my external data can't available for
vignette data, and vignette compilation is failed again. I used
system.file() to do this, but not working. Any idea please ? How can I
overcome this problem? Thanks a lot to Bioconductor project team.

Best regards :

Jurat


On Fri, Dec 2, 2016 at 5:20 PM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:

> If your package is in github at https://github.com/julaiti/MSPC , it
> looks like there is no inst or extdata folder in that repository.
>
> Maybe it has not yet been added/committed/pushed to 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 with:
>
> extdata/
> foo.txt
>
> HTH
> Dan
>
>
> - Original Message -
> > From: "Jurat Shayidin" <juratb...@gmail.com>
> > To: "Hervé Pagès" <hpa...@fredhutch.org>, "bioc-devel" <
> bioc-devel@r-project.org>
> > Sent: Friday, December 2, 2016 5:36:28 AM
> > Subject: Re: [Bioc-devel] package vignette error : external data can't
> be captured when compiling package vignette
>
> > Dear Hervé :
> >
> > Thanks again for your response on my issue. I've read your message very
> > carefully and did all you suggested to me, still can't fix the vignette
> > compilation error. I have developed my package on windows machine under
> > devel version of R and Bioc, all unit test works fine to me. I don't
> > understand why inst/ directory was not created when I build and install
> my
> > packages, external data can't be read during vignette compilation.
> > However, my objective is, to build my package vignette with no error in
> the
> > first place, then continue to edit the context until getting final
> version
> > of vignette file. When I install packages using devtools::install(), I
> got
> > this :
> >
> >> devtools::install()
> > Installing MSPC
> > "C:/PROGRA~1/R/R-devel/bin/x64/R" \
> > --no-site-file --no-environ --no-save \
> > --no-restore --quiet CMD INSTALL \
> > "C:/Users/jvrat/Documents/MSPC" \
> > --library="C:/Users/jvrat/Documents/R/win-library/3.4" \
> > --install-tests
> > * installing *source* package 'MSPC' ...
> > ** R
> > ** tests
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** installing vignettes
> > ** testing if installed package can be loaded
> > * DONE (MSPC)
> > Reloading installed MSPC
> >
> >
> 

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Jurat Shayidin]

Dear Hervé :

Thanks again for your response on my issue. I've read your message very
carefully and did all you suggested to me, still can't fix the vignette
compilation error. I have developed my package on windows machine under
devel version of R and Bioc, all unit test works fine to me. I don't
understand why inst/ directory was not created when I build and install my
packages, external data can't be read during vignette compilation.
However, my objective is, to build my package vignette with no error in the
first place, then continue to edit the context until getting final version
of vignette file. When I install packages using devtools::install(), I got
this :

> devtools::install()
Installing MSPC
"C:/PROGRA~1/R/R-devel/bin/x64/R" \
--no-site-file --no-environ --no-save \
--no-restore --quiet CMD INSTALL \
"C:/Users/jvrat/Documents/MSPC" \
--library="C:/Users/jvrat/Documents/R/win-library/3.4" \
--install-tests
* installing *source* package 'MSPC' ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSPC)
Reloading installed MSPC


I believe doing this is right in vignette file after I follow your advise :

```{r}
library(MSPC)
inputBed <- list.files(system.file("extdata", package = "MSPC"), full.names
= TRUE)
inputData <- readPeakFile(peakFolder = inputBed)

inputData
```


However, I should not add inst/extdata manually , without this I can't
allow to load external data for package use, and vignette compilation keep
failed. To be honest, this is my very first time building R packages, I
don't know how to fix this error. Just out of curiosity, during package
installation, everything is under the inst/ , but I don't have this folder.
Why is that ? Is that possible to get further help from Bioconductor
project team to review the package source in github ?

I am stuck with this problem, I searched all possible answer from all over
the place, cannot fix my issues. I am very sorry if my question is naive to
ask here. Could you point me out how to possibly solve this problem? Thanks
again for your great favor.

Best regards :

Jurat



On Fri, Dec 2, 2016 at 2:04 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:

> Hi,
>
> Make sure you understand the difference between the *package source
> tree*, which you control and where you must create the inst/ folder,
> and the *package installation folder*, which gets created and
> populated by 'R CMD INSTALL'. The exact location of the *package
> installation folder* doesn't really matter but if you are curious
> you can use the .libPaths() command to see it. The *package installation
> folder* is the subfolder of .libPaths() that has the name of the
> package. You can also see it with find.package("mypackage").
>
> During installation, everything that is under the inst/ folder will
> get installed *directly* under the *package installation folder*.
> So if you created the extdata/ folder under inst/ (as it should be),
> extdata/ will end up being installed at .libPaths()/mypackage/extdata/
> The code in your examples can get the path to the *installed* extdata/
> folder with
>
>   system.file(package="mypackage", "extdata")
>
> or get the path to any file under extdata/ with e.g.
>
>   system.file(package="mypackage", "extdata", "data1.bed")
>
> Don't do
>
>   system.file(package="mypackage", "extdata/data1.bed")
>
> even if it works for you because it's not portable (the use of / as
> a separator is a platform-dependent thing).
>
> Finally note that you should never 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.
>
>
> On 12/01/2016 04:34 PM, Jurat Shayidin wrote:
>
>> 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::install()command
>> to install my packages, but installation directory inst/ was not created
>> automatically. By R package convention, all external data must be located
>> in inst/, so I manually created this folder  inst/extdata and paste my
>> data, but vignette compilation still failed. According to convention of R
>> package, my package structure will be:
>>
>> myPacka

[Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Jurat Shayidin]

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::install()command
to install my packages, but installation directory inst/ was not created
automatically. By R package convention, all external data must be located
in inst/, so I manually created this folder  inst/extdata and paste my
data, but vignette compilation still failed. According to convention of R
package, my package structure will be:

myPackage
`- inst
`- extdata
`- data1.bed
`- data2.bed
`- R
`- ...
`- NAMESPACE
`- DESCRIPTION

-- 

Note that readPeakFile take list of bed file as an input. Here is the toy
function I am going to use in vignette file .

readPeakFile<- function(mydat, ...) {
  files <- list.files(mydat, full.names = TRUE, "\\.bed$")
  readMe <- lapply(files, import.bed)
  return(readMe)}

I got error from this code chunk :

```{r}
library(MSPC)
inputBed <- list.files(system.file("extdata", package = "MSPC"), full.names
= TRUE)
inputData <- readPeakFile(peakFolder = inputBed)

inputData
```

Error: object 'inputData' not found

I tried another way which discussed in mailing list long time ago, but I
got empty list instead :

```{r}
library(MSPC)
extdata.dir <- system.file("extdata", package = "MSPC")
bedfiles <- dir(extdata.dir, pattern="\\.bed$", full.names=TRUE)
myData <- readPeakFiles(peakFolder = bedfiles)

myData
```
named list()

can't figure out why got these issue very often. why installation directory
inst not created automatically ? why test data can't be captured by
system.file() when compiling the package vignette ? I think inst must be
created automatically when I install my packages, but it didn't happen to
me, why is that ? How can I fix this compilation error for package vignette
? Any idea please ?

Here is what I got :

==> devtools::check()

Updating MSPC documentation
Loading MSPC
Writing NAMESPACE
Writing FDR_stats.Rd
Writing Fisher_stats.Rd
Writing MSPC-package.Rd
Writing info.Rd
Writing create_output.Rd
Writing denoise_ERs.Rd
Writing filterByFisherMethod.Rd
Writing filterByOverlapHit.Rd
Writing peakOverlapping.Rd
Writing pvalueConversion.Rd
Writing readPeakFiles.Rd
Setting env vars
---
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building MSPC
--
"C:/PROGRA~1/R/R-devel/bin/x64/R" --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD build "C:\Users\jvrat\Documents\MSPC"  \
  --no-resave-data --no-manual

* checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
* preparing 'MSPC':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 46-52 (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
length(peakFolder) > 0 is not TRUE
Execution halted
Warning: running command '"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla
--default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"'
had status 1
Error: Command failed (1)
In addition: Warning message:
@importfrom [peakOverlapping.R#23]: unknown tag
Execution halted

Exited with status 1.




Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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[Bioc-devel] unexpected error : BiocInstaller - unable to access the index for reporitory

[Jurat Shayidin]

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
warning sometime prevent to install package from Bioconductor. Can anyone
help me what's going on?  Thanks a lot

> BiocInstaller::biocValid()
Warning: unable to access index for repository
https://bioconductor.org/packages/3.5/data/annotation/src/contrib:
  cannot open URL '
https://bioconductor.org/packages/3.5/data/annotation/src/contrib/PACKAGES'

Here is session info :

> sessionInfo()
R Under development (unstable) (2016-11-13 r71655)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] SummarizedExperiment_1.5.3 Biobase_2.35.0
[3] rtracklayer_1.35.1 GenomicRanges_1.27.6
[5] GenomeInfoDb_1.11.4IRanges_2.9.8
[7] S4Vectors_0.13.2   BiocGenerics_0.21.0
[9] BiocInstaller_1.25.2

loaded via a namespace (and not attached):
 [1] lattice_0.20-34  XML_3.98-1.5
 [3] Rsamtools_1.27.2 Biostrings_2.43.0
 [5] GenomicAlignments_1.11.1 bitops_1.0-6
 [7] grid_3.4.0   zlibbioc_1.21.0
 [9] XVector_0.15.0   Matrix_1.2-7.1
[11] BiocParallel_1.9.1   tools_3.4.0
[13] RCurl_1.95-4.8   compiler_3.4.0
>

-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Jurat Shayidin]

Dear Kasper :
Thanks for your explanation. However, I opened the shell from Rstudio and
type the command R --vanilla, seems it works fine, but still not sure about
efficiency of using R -vanilla. I am not confident about using R commands,
so is there any quick example that I can practice and understand this in
depth ? Thanks a lot

Best regards:
Jurat

On Fri, Nov 11, 2016 at 7:22 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> You're bing asked to use
>   R --vanilla
> because you have a non-standard problem, exemplified by the fact that what
> you have problems with (installing CRAN packages) works for thousands of
> users of Bioconductor (certainly for me).  This suggests that there is
> something wrong with something on your computer.  Starting R with R
> --vanilla disables loading of some user-specific component. If it works
> 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 Shayidin <juratb...@gmail.com>
> wrote:
>
>> 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. Could you please
>> elaborate
>> >> your answer on my doubt ? Thanks
>> >>
>> >> 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, 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 instead. Is this correct ? I didn't clean R
>> session,
>> >>>>
>> >>>
>> > this is not related to your original question. I personally need both a
>> > release and devel version of R and have both installed.
>> >
>> > how can I make it happen on windows?  Plus, How to make R session
>> >>>> vanilla ? What's right configuration both R devel and Bioc devel
>> before
>> >>>>
>> >>>
>> > open a Windows shell ('cmd') and type
>> >
>> >   R --vanilla
>> >
>> > or perhaps
>> >
>> >   Rgui --vanilla
>> >
>> > building my packages ? Could you elaborate your answer please? Thank you
>> >>>>
>> >>>
>> > again, this isn't related to your original question. See the section
>> > 'Which version of R?' in
>> >
>> >   http://bioconductor.org/developers/how-to/useDevel/
>> >
>> > Martin
>> >
>> >
>> > very much
>> >>>>
>> >>>> Best regards :
>> >>>>
>> >>>> On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
>> >>>> <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org
>> >>
>> >>>>
>> >>>> wrote:
>> >>>>
>> >>>> On 11/11/2016 09:44 AM, Jurat Shayidin wrote:
>> >>>>
>> >>>> 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
>> >>>> devel
>> >>>> version of Bioc and R, so I did it. But can't installl
>> packages
>> >>>> from CRAN
>> >>>> like dplyr. How can I overcome this issue ? Any quick
>> solution
>> >>>> ?  I got
&

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Jurat Shayidin]

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. Could you please elaborate
>> your answer on my doubt ? Thanks
>>
>> 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, 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 instead. Is this correct ? I didn't clean R session,
>>>>
>>>
> this is not related to your original question. I personally need both a
> release and devel version of R and have both installed.
>
> how can I make it happen on windows?  Plus, How to make R session
>>>> vanilla ? What's right configuration both R devel and Bioc devel before
>>>>
>>>
> open a Windows shell ('cmd') and type
>
>   R --vanilla
>
> or perhaps
>
>   Rgui --vanilla
>
> building my packages ? Could you elaborate your answer please? Thank you
>>>>
>>>
> again, this isn't related to your original question. See the section
> 'Which version of R?' in
>
>   http://bioconductor.org/developers/how-to/useDevel/
>
> Martin
>
>
> very much
>>>>
>>>> Best regards :
>>>>
>>>> On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
>>>> <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
>>>>
>>>> wrote:
>>>>
>>>> On 11/11/2016 09:44 AM, Jurat Shayidin wrote:
>>>>
>>>> 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
>>>> devel
>>>> version of Bioc and R, so I did it. But can't installl packages
>>>> from CRAN
>>>> like dplyr. How can I overcome this issue ? Any quick solution
>>>> ?  I got
>>>> error as follow:
>>>>
>>>>
>>>> BiocInstaller::useDevel()
>>>>
>>>> Error: 'devel' version already in use
>>>>
>>>> install.packages("dplyr")
>>>>
>>>> Error in install.packages : missing value where TRUE/FALSE
>>>> needed
>>>>
>>>>
>>>> this does not happen for me; you'll need to debug on your end,
>>>> minimally, reporting the output of traceback() after the error
>>>> occurs.
>>>>
>>>> are you in a clean R session with no .RData or other objects loaded
>>>> that might interfere with R?
>>>>
>>>>   R --vanilla
>>>>
>>>> Martin
>>>>
>>>> PS -- please do not 'close' questions that have been answered on
>>>> support.bioconductor.org <http://support.bioconductor.org>.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> sessionInfo()
>>>>
>>>> R Under development (unstable) (2016-11-09 r71642)
>>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>> Running under: Windows >= 8 x64 (build 9200)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_United States.1252
>>>> [2] LC_CTYPE=English_United States.1252
>>>> [3] LC_MONETARY=English_United States.1252
>>>> [4] LC_NUMERIC=C
>>>> [5] LC_TIME=English_United States.1252
>>>>
>>>> attached base packages:
>>>> [1] parallel  stats4stats graphics  grDevices
>>>> [6] utils datasets  methods   base
>>&

Re: [Bioc-devel] can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Jurat Shayidin]

Thanks for reminding, I'll keep this in mind. I figured out that after
clean R session, problem is solved. But how can I avoid this sort of issue
and facilitate the building package ? How can make R session vanilla ? Any
recommendation for configuration before start building packages ? Could 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 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 instead. Is this correct ? I didn't clean R session,
>> how can I make it happen on windows?  Plus, How to make R session
>> vanilla ? What's right configuration both R devel and Bioc devel before
>> building my packages ? Could you elaborate your answer please? Thank you
>> very much
>>
>> Best regards :
>>
>> On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
>> <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
>>
>> wrote:
>>
>> On 11/11/2016 09:44 AM, Jurat Shayidin wrote:
>>
>> 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
>> devel
>> version of Bioc and R, so I did it. But can't installl packages
>> from CRAN
>> like dplyr. How can I overcome this issue ? Any quick solution
>> ?  I got
>> error as follow:
>>
>>
>> BiocInstaller::useDevel()
>>
>> Error: 'devel' version already in use
>>
>> install.packages("dplyr")
>>
>> Error in install.packages : missing value where TRUE/FALSE needed
>>
>>
>> this does not happen for me; you'll need to debug on your end,
>> minimally, reporting the output of traceback() after the error occurs.
>>
>> are you in a clean R session with no .RData or other objects loaded
>> that might interfere with R?
>>
>>   R --vanilla
>>
>> Martin
>>
>> PS -- please do not 'close' questions that have been answered on
>> support.bioconductor.org <http://support.bioconductor.org>.
>>
>>
>>
>>
>>
>> sessionInfo()
>>
>> R Under development (unstable) (2016-11-09 r71642)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows >= 8 x64 (build 9200)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] parallel  stats4stats graphics  grDevices
>> [6] utils datasets  methods   base
>>
>> other attached packages:
>>  [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
>>  [3] XVector_0.15.0 rtracklayer_1.35.1
>>  [5] GenomicRanges_1.27.5   GenomeInfoDb_1.11.3
>>  [7] IRanges_2.9.7  S4Vectors_0.13.2
>>  [9] BiocGenerics_0.21.0BiocInstaller_1.25.2
>>
>> loaded via a namespace (and not attached):
>>  [1] lattice_0.20-34  XML_3.98-1.5
>>  [3] Rsamtools_1.27.2 Biostrings_2.43.0
>>  [5] GenomicAlignments_1.11.0 bitops_1.0-6
>>  [7] grid_3.4.0   zlibbioc_1.21.0
>>  [9] Matrix_1.2-7.1   BiocParallel_1.9.1
>> [11] tools_3.4.0  RCurl_1.95-4.8
>> [13] compiler_3.4.0
>>
>>
>>
>>
>>
>>
>>
>> This email message may contain legally privileged and/or
>> confidential information.  If you are not the intended recipient(s),
>> or the employee or agent responsible for the delivery of this
>> message to the intended recipient(s), you are hereby notified that
>>   

[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Jurat Shayidin]

I'll keep this in mind. Thanks for reminding. Could you please elaborate
your answer on my doubt ? Thanks

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, 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 instead. Is this correct ? I didn't clean R session,
>> how can I make it happen on windows?  Plus, How to make R session
>> vanilla ? What's right configuration both R devel and Bioc devel before
>> building my packages ? Could you elaborate your answer please? Thank you
>> very much
>>
>> Best regards :
>>
>> On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
>> <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
>>
>> wrote:
>>
>> On 11/11/2016 09:44 AM, Jurat Shayidin wrote:
>>
>> 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
>> devel
>> version of Bioc and R, so I did it. But can't installl packages
>> from CRAN
>> like dplyr. How can I overcome this issue ? Any quick solution
>> ?  I got
>> error as follow:
>>
>>
>> BiocInstaller::useDevel()
>>
>> Error: 'devel' version already in use
>>
>> install.packages("dplyr")
>>
>> Error in install.packages : missing value where TRUE/FALSE needed
>>
>>
>> this does not happen for me; you'll need to debug on your end,
>> minimally, reporting the output of traceback() after the error occurs.
>>
>> are you in a clean R session with no .RData or other objects loaded
>> that might interfere with R?
>>
>>   R --vanilla
>>
>> Martin
>>
>> PS -- please do not 'close' questions that have been answered on
>> support.bioconductor.org <http://support.bioconductor.org>.
>>
>>
>>
>>
>>
>> sessionInfo()
>>
>> R Under development (unstable) (2016-11-09 r71642)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows >= 8 x64 (build 9200)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] parallel  stats4stats graphics  grDevices
>> [6] utils datasets  methods   base
>>
>> other attached packages:
>>  [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
>>  [3] XVector_0.15.0 rtracklayer_1.35.1
>>  [5] GenomicRanges_1.27.5   GenomeInfoDb_1.11.3
>>  [7] IRanges_2.9.7  S4Vectors_0.13.2
>>  [9] BiocGenerics_0.21.0BiocInstaller_1.25.2
>>
>> loaded via a namespace (and not attached):
>>  [1] lattice_0.20-34  XML_3.98-1.5
>>  [3] Rsamtools_1.27.2 Biostrings_2.43.0
>>  [5] GenomicAlignments_1.11.0 bitops_1.0-6
>>  [7] grid_3.4.0   zlibbioc_1.21.0
>>  [9] Matrix_1.2-7.1   BiocParallel_1.9.1
>> [11] tools_3.4.0  RCurl_1.95-4.8
>> [13] compiler_3.4.0
>>
>>
>>
>>
>>
>>
>>
>> This email message may contain legally privileged and/or
>> confidential information.  If you are not the intended recipient(s),
>> or the employee or agent responsible for the delivery of this
>> message to the intended recipient(s), you are hereby notified that
>> any disclosure, copying, distribution, or use of this email message
>> is prohibited.  If you have received this message in error, please
>> notify the sender immediately by e-mail and delete this email
>> message fr

[Bioc-devel] can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Jurat Shayidin]

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 devel
version of Bioc and R, so I did it. But can't installl packages from CRAN
like dplyr. How can I overcome this issue ? Any quick solution ?  I got
error as follow:


> BiocInstaller::useDevel()
Error: 'devel' version already in use
> install.packages("dplyr")
Error in install.packages : missing value where TRUE/FALSE needed
>

> sessionInfo()
R Under development (unstable) (2016-11-09 r71642)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel  stats4stats graphics  grDevices
[6] utils datasets  methods   base

other attached packages:
 [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
 [3] XVector_0.15.0 rtracklayer_1.35.1
 [5] GenomicRanges_1.27.5   GenomeInfoDb_1.11.3
 [7] IRanges_2.9.7  S4Vectors_0.13.2
 [9] BiocGenerics_0.21.0BiocInstaller_1.25.2

loaded via a namespace (and not attached):
 [1] lattice_0.20-34  XML_3.98-1.5
 [3] Rsamtools_1.27.2 Biostrings_2.43.0
 [5] GenomicAlignments_1.11.0 bitops_1.0-6
 [7] grid_3.4.0   zlibbioc_1.21.0
 [9] Matrix_1.2-7.1   BiocParallel_1.9.1
[11] tools_3.4.0  RCurl_1.95-4.8
[13] compiler_3.4.0
>



-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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[Bioc-devel] can't fix the bug: Error: 'devel' version requires a more recent R

[Jurat Shayidin]

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,
problem can't solved still. How can I overcome this issue ? Here is the
session info:


> useDevel()
Error: 'devel' version requires a more recent R

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] rtracklayer_1.34.1   GenomicRanges_1.26.1 BiocInstaller_1.24.0
[4] GenomeInfoDb_1.10.0  IRanges_2.8.0S4Vectors_0.12.0
[7] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-33XML_3.98-1.4
 [3] Rsamtools_1.26.1   Biostrings_2.42.0
 [5] GenomicAlignments_1.10.0   bitops_1.0-6
 [7] grid_3.3.1 zlibbioc_1.20.0
 [9] XVector_0.14.0 Matrix_1.2-6
[11] BiocParallel_1.8.1 tools_3.3.1
[13] Biobase_2.34.0 RCurl_1.95-4.8
[15] SummarizedExperiment_1.4.0


-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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[Bioc-devel] memory inefficiency problem of building MSPC packages

[Jurat Shayidin]

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 for
multiple GRanges objects simultaneously and proceed joint analysis for
multiple ChIP-Seq sample to rescue weak enriched region by helping with
co-localized evidence of multiple GRanges . After I reviewed all my source
code, indeed some paired overlap repeated many times that cause unnecessary
memory usage.
This is my custom function that I developed, it works perfectly in my
current workflow, but cause memory inefficiency problem.

grs <- GRangeslist(gr1, gr2, gr3, gr4, ...)

overlap <- function(grs, idx=1L, FUN=which.min) {
  chosen <- grs[[idx]]
  que.hit <- as(findOverlaps(chosen), "List")
  sup.hit <- lapply(grs[-idx], function(ele_) {
ans <- as(findOverlaps(chosen, ele_), "List")
out.idx0 <- as(FUN(extractList(ele_$p.value, ans)), "List")
out.idx0 <- out.idx0[!is.na(out.idx0)]
ans <- ans[out.idx0]
  })
  res <- c(list(que.hit), sup.hit)
  return(res)
}

How can I optimize my custom function without memory inefficiency? How can
I get rid of repeated overlapped paired GRanges? How can I efficiently
solve this issue? Can anyone propose possible ideas to get through this
problem? Thanks a lot



-- 
Jurat Shahidin
Ph.D. candidate
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano

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[Bioc-devel] FDR estimation for Biological ChIP-Seq replicate in the context of GRanges.

[Jurat Shayidin]

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 this is general
workflow that I have implemented in my packages.

in the context of processing three GRanges object for finding
colocalization evidence across these sample, and this is the general
workflow:

-> read & load multiple sample (bed format) in GRanges  - > find overlapped
regions conditionally in parallel -> filtering function with specific
threshold value (a.k.a, count overall overlapped regions in parallel) ->
chisq.test() for data that passed from previous step- > based on the
combined pvalue, further filtering process with second threshold value
(data that passed from previous step) - > final output as GRanges (preserve
data who also passed from previous step, but not export them to hard disk)

first running of my packages are: (a as chosenSample, b,c are
supportingSamples):

ov_ab_1 <- as(findOverlaps(a, b), "List")
ov_ac_1 <- as(findOverlaps(a, c), "List")

in second running of my packages, I have to switch parameter (where b as
chosenSample, a,c are supportingSample), such as:

ov_ba_2 <- as(findOverlaps(b,a), "List")
ov_bc_2 <- as(findOverlaps(b,c), "List")

in the third running test, I am gonna do like this (where c as
chosenSample, a,b are supportingSample)):

ov_ca_3 <- as(findOverlaps(c,a), "List")
ov_cb_3 <- as(findOverlaps(c,b), "List")

However, implementing FDR estimation for a, b, c from first , second, third
running test, where each processed sample has three different output :

for example:
a_preserved_first_test, a_preserved_second_test, a_preserved_third_test and
same ouput format for b, c respectively

*Objective*: in the context of Biological replicates, I want to retrieve
common regions that found at least two running test (but how, I am seeking
solution for them), then pass these regions to p.adjust() to get adjusted
pvalue, then do further filtering process with third threshold value, and
generate output for these regions that passed previous step finally .

*Question*:

In order to do FDR estimation, I need to run my packages three times (if
three sample are an input), where I may put result of each test into
specific R environment (I am not sure this is right things to do). Is there
any possible optimizing approach regarding running my packages three times
(any chance to recursively switch to next running test when previous
running test is done).?

I am not sure if I create sub-environment where saving the result of each
running test. I hope there might be better solution.  Maybe my question is
bit of straightforward to you, forgive my naive question if it was. Any
possible  approach, suggestion, trivial solution or any recommended
bioconductor packages may help out above question, that are highly
appreciated. Thank a lot

Best regards

-- 
Jurat Shahidin
Ph.D. candidate
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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[Bioc-devel] [Bio-dev]: how to iterate and index set of bed files ?

[Jurat Shayidin]

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
length, and goal is to process multiple sample in parallel.
*my input parameter is set of bed files, when I am gonna index first bed
files as querySample, while rest of bed files are being as targetSample. I
used findOverlaps function from GenomicRanges packages, when all features
from querySample are overlapped with all features from targetSample, report
overlapped peak and generate new bed files to save them , then chose second
bed file as QuerySaple, while chose others as targetSample, repeat above
process. *
here is my question, hope dear member give me some idea how to get out this
problem. *how to iterate and index set of bedFiles?*
*FYI, I carefully read posting guide for how to ask question in Bio-Dev
mailing list, if I made mistake on that, I will be appreciate if someone
remind me. Many thanks to all of you*
 I think there is set of combination, such as below:
bed.1 parallel map to (bed.2, bed.3, bed.4)
bed.2 parallel map to (bed.1, bed.3, bed.4)
bed.3 parallel map to (bed.1, bed.2, bed.4)
bed.4 parallel map to (bed.1, bed.2, bed.3)

for example, this my R code:

indexSample <- function(bedFiles, desDir=getwd(), verbose=FALSE){
  if(is(bedFiles %in% desDir)){
file <- list.files(path = bedFiles)
idx <- unlist(sapply("bed", grep, file))
idx <- sort(unique(idx))
bedFiles <- file[idx]

for(j in 1:length(bedFiles)){
  qSample <- bedFiles[1]# chosen querySample bed file
  qIdx <- which(j==qSample)
  if(!is(qSample[1],"GRanges")){
qSample.gr <- loadSample(qSample)   # loadSample to read bed file
as GRanges objects
  }
  else{
qSample.gr <- qSample
  }
  # there is code that access all features of qSample [I have done
already]

  for(jj in 2:length(bedFiles)){
tSample <- bedFiles[jj]  # rest of bed files (multiple)
# there is code that put all features of tSample in GNCList object
[I have done]
  }
  # then call findOverlap from GenomicRanges packages
}
  }
  # return result of first case
}






-- 
Jurat Shahidin
Ph.D. candidate
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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