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

[Hervé Pagès]

Let's keep the discussion on the mailing list.

On 12/07/2016 10:58 PM, Stian Lågstad wrote:

I tried doing that now and got another error: "cannot open the
connection". I don't know how to investigate that further.
Link to new build
report: 
http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161208015500.html


At least the webshot issue is gone. Yes adding it to the Suggests
field is of course a dirty hack. The hope being that it would help
you quickly work around the build failure on oaxaca.



Do you think the issue could be caused by the warning below? Since I'm
only seeing that on oaxaca.
"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."


Both pandoc and pandoc-citeproc are on oaxaca:

  oaxaca:~ biocbuild$ which pandoc
  /usr/local/bin/pandoc
  oaxaca:~ biocbuild$ which pandoc-citeproc
  /usr/local/bin/pandoc-citeproc

And pandoc version is >= 1.12.3:

  oaxaca:~ biocbuild$ pandoc -v | head -n 2
  pandoc 1.17.0.2
  Compiled with texmath 0.8.5, highlighting-kate 0.6.2.

Also we don't see that warning on the daily builds even though
many packages use pandoc/pandoc-citeproc for their vignettes.

So again, I'm not sure what's going on, sorry. Likely a problem on
our side. I suggest you ignore this build error on oaxaca for now.

Cheers,
H.



Thank you.

On Thu, Dec 8, 2016 at 1:07 AM, Hervé Pagès > wrote:

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:

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

[Andrzej Oleś]

Dear Stian,
according to https://github.com/yihui/knitr/releases/tag/v1.14 the
dependency on webshot, which apparently is used to take website
screenshots, is optional and knitr should use fallback mode if webshot is
not available. Webshot has a list of system dependencies, not sure how hard
to fulfill. I wouldn't recommend adding webshot dependency to your packge,
unless you actually intended to use the functionality provided by it.

Cheers,
Andrzej



On Thu, Dec 8, 2016 at 1:07 AM, Hervé Pagès  wrote:

> 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
>> > 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
>> > 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
>> 
>>
>>
>> --
>>  

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

[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
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mailing list
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--
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?

[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]]

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

[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


___
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--
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?

[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

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

[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]]

___
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