Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck
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
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<mailto: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<mailto:juratb...@gmail.com>>
Sent: Friday, December 16, 2016 6:06:41 AM
To: Shepherd, Lori; bioc-devel@r-project.org<mailto: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<mailto: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
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
>
> 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
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<mailto: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<mailto:bioc-devel-boun...@r-project.org>> on
behalf of Jurat Shayidin <juratb...@gmail.com<mailto:juratb...@gmail.com>>
Sent: Thursday, December 15, 2016 7:17:42 AM
To: bioc-devel@r-project.org<mailto: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
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 on behalf of Jurat
> Shayidin
> *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 , 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>
>
> [[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
Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck
$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 on behalf of Jurat Shayidin
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 , 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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