Re: [Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

2016-12-07 Thread Hervé Pagès 

Not clear to me what's going on, I'm not a knitr/rmarkdown expert.
What I see is that knitr suggests webshot probably because it needs
it in some situations. That must be a rare situation though because
webshot is not installed on our build machines, which means that none
of the 1298 software packages currently in BioC devel needs it.

So I'm not sure why it would need it for building your vignette, and
why it would need it only on oaxaca. Anyway maybe it would help to add
webshot to your Suggests field. That will trigger installation of
webshot by the SPB before it tries to build/check your package.
Don't forget to bump again the package version in order to trigger
a new build by the SPB.

H.

On 12/07/2016 12:31 PM, Stian Lågstad wrote:

Thank you both. Could you also advice me on the error I'm receiving
on oaxaca? "there is no package called 'webshot'"
New build
report: 
http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161207152203.html


On Wed, Dec 7, 2016 at 7:42 PM, Hervé Pagès > wrote:

Hi Stian,

The build machines used by the SPB are the same as the machines used
for the daily builds and they already have the latest BiocStyle
installed (BiocStyle 2.3.23). You can see this by going on the daily
build report for devel and clicking on any of the link in the
"Installed pkgs" column in the top table:

  https://bioconductor.org/checkResults/3.5/bioc-LATEST/


However, the SPB report for your package is from Nov 30 so it could
be that it predates the fix in BiocStyle. You can trigger a new build
of your package by just bumping its version on github.

Hope this helps,
H.


On 12/07/2016 07:17 AM, Leonardo Collado Torres wrote:

Hi Stian,

Install BiocStyle 2.3.20 or newer and that error will go away. See
https://github.com/Bioconductor/BiocStyle/issues/20
 for details.

Best,
Leo

On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad
> wrote:

Hi,

Could someone please advice me on the errors I'm getting
building my
package? I'm unable to reproduce them locally.

Link to build report:

http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html


Link to bioconductor submission issue:
https://github.com/Bioconductor/Contributions/issues/206


I'm getting an error on creating my vignette: `argumemt is
not a character
vector`
I also get this: `there is no package called 'webshot'`

I believe these could be related to this warning: `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.`

I use rmarkdown_1.2 locally without problems. Can someone
here assist me?

Thank you.

--
Stian Lågstad
+47 41 80 80 25 

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org 
mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



___
Bioc-devel@r-project.org 
mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org 
Phone:  (206) 667-5791 
Fax:(206) 667-1319 




--
Stian Lågstad
+47 41 80 80 25


--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

2016-12-07 Thread Stian Lågstad 
Thank you both. Could you also advice me on the error I'm receiving
on oaxaca? "there is no package called 'webshot'"
New build report: http://bioconductor.org/spb_reports/chimeraviz_
buildreport_20161207152203.html

On Wed, Dec 7, 2016 at 7:42 PM, Hervé Pagès  wrote:

> Hi Stian,
>
> The build machines used by the SPB are the same as the machines used
> for the daily builds and they already have the latest BiocStyle
> installed (BiocStyle 2.3.23). You can see this by going on the daily
> build report for devel and clicking on any of the link in the
> "Installed pkgs" column in the top table:
>
>   https://bioconductor.org/checkResults/3.5/bioc-LATEST/
>
> However, the SPB report for your package is from Nov 30 so it could
> be that it predates the fix in BiocStyle. You can trigger a new build
> of your package by just bumping its version on github.
>
> Hope this helps,
> H.
>
>
> On 12/07/2016 07:17 AM, Leonardo Collado Torres wrote:
>
>> Hi Stian,
>>
>> Install BiocStyle 2.3.20 or newer and that error will go away. See
>> https://github.com/Bioconductor/BiocStyle/issues/20 for details.
>>
>> Best,
>> Leo
>>
>> On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad 
>> wrote:
>>
>>> Hi,
>>>
>>> Could someone please advice me on the errors I'm getting building my
>>> package? I'm unable to reproduce them locally.
>>>
>>> Link to build report:
>>> http://bioconductor.org/spb_reports/chimeraviz_buildreport_
>>> 20161130173413.html
>>> Link to bioconductor submission issue:
>>> https://github.com/Bioconductor/Contributions/issues/206
>>>
>>> I'm getting an error on creating my vignette: `argumemt is not a
>>> character
>>> vector`
>>> I also get this: `there is no package called 'webshot'`
>>>
>>> I believe these could be related to this warning: `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.`
>>>
>>> I use rmarkdown_1.2 locally without problems. Can someone here assist me?
>>>
>>> Thank you.
>>>
>>> --
>>> Stian Lågstad
>>> +47 41 80 80 25
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>



-- 
Stian Lågstad
+47 41 80 80 25

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

2016-12-07 Thread Hervé Pagès 

Hi Stian,

The build machines used by the SPB are the same as the machines used
for the daily builds and they already have the latest BiocStyle
installed (BiocStyle 2.3.23). You can see this by going on the daily
build report for devel and clicking on any of the link in the
"Installed pkgs" column in the top table:

  https://bioconductor.org/checkResults/3.5/bioc-LATEST/

However, the SPB report for your package is from Nov 30 so it could
be that it predates the fix in BiocStyle. You can trigger a new build
of your package by just bumping its version on github.

Hope this helps,
H.

On 12/07/2016 07:17 AM, Leonardo Collado Torres wrote:

Hi Stian,

Install BiocStyle 2.3.20 or newer and that error will go away. See
https://github.com/Bioconductor/BiocStyle/issues/20 for details.

Best,
Leo

On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad  wrote:

Hi,

Could someone please advice me on the errors I'm getting building my
package? I'm unable to reproduce them locally.

Link to build report:
http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html
Link to bioconductor submission issue:
https://github.com/Bioconductor/Contributions/issues/206

I'm getting an error on creating my vignette: `argumemt is not a character
vector`
I also get this: `there is no package called 'webshot'`

I believe these could be related to this warning: `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.`

I use rmarkdown_1.2 locally without problems. Can someone here assist me?

Thank you.

--
Stian Lågstad
+47 41 80 80 25

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

2016-12-07 Thread Leonardo Collado Torres 
Hi Stian,

Install BiocStyle 2.3.20 or newer and that error will go away. See
https://github.com/Bioconductor/BiocStyle/issues/20 for details.

Best,
Leo

On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad  wrote:
> Hi,
>
> Could someone please advice me on the errors I'm getting building my
> package? I'm unable to reproduce them locally.
>
> Link to build report:
> http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html
> Link to bioconductor submission issue:
> https://github.com/Bioconductor/Contributions/issues/206
>
> I'm getting an error on creating my vignette: `argumemt is not a character
> vector`
> I also get this: `there is no package called 'webshot'`
>
> I believe these could be related to this warning: `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.`
>
> I use rmarkdown_1.2 locally without problems. Can someone here assist me?
>
> Thank you.
>
> --
> Stian Lågstad
> +47 41 80 80 25
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

2016-12-07 Thread Stian Lågstad 
Hi,

Could someone please advice me on the errors I'm getting building my
package? I'm unable to reproduce them locally.

Link to build report:
http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html
Link to bioconductor submission issue:
https://github.com/Bioconductor/Contributions/issues/206

I'm getting an error on creating my vignette: `argumemt is not a character
vector`
I also get this: `there is no package called 'webshot'`

I believe these could be related to this warning: `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.`

I use rmarkdown_1.2 locally without problems. Can someone here assist me?

Thank you.

-- 
Stian Lågstad
+47 41 80 80 25

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel