[Bioc-devel] Error in Vignette of package

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit :

Thanks for the answer. However replacing it resulted in another error for me:

Quitting from lines 2-41 (MACPET.Rmd) 
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> eval -> eval
Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis Vardaxis <iova89 at hotmail.com>
Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package
 
Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay" <bioc-devel-bounces at r-project.org on behalf of b2tremblay at uwaterloo.ca> wrote:

    I?ve been getting the exact same error for compiling the Rmarkdown
    vignettes in my own package. Some partial testing before the weekend
    revealed that in my case the error could be circumvented simply by not
    using
    
        output: BiocStyle::pdf_document
    
    but instead
    
        output: pdf_document
    
    in the yaml header. I?m not quite sure why, but when BiocStyle is used
    some of the latex code for code highlighting is repeated, leading to the
    'already defined' error. I?ve not updated my package since before this
    error started.
    
    BT
    

    > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit :
    > 
    > Hey,
    > 
    > I am trying to build my package Vegnette and I get the following error:
    > 
    > ! LaTeX Error: Command \VerbBar already defined.
    >               Or name \end... illegal, see p.192 of the manual.
    > 
    > I tried to find what this means with no luck.
    > 
    > Best,
    > Ioannis
    > 
    > 
    >    [[alternative HTML version deleted]]
    > 
    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/bioc-devel

Not using BiocStyle::pdf_document means you can?t use the helpers/macros.
Try this in a fresh interactive session:

  library(BiocStyle)
  rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue is and
thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit :

Thanks for the answer. However replacing it resulted in another error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

    I?ve been getting the exact same error for compiling the Rmarkdown
    vignettes in my own package. Some partial testing before the weekend
    revealed that in my case the error could be circumvented simply by

not

    using

        output: BiocStyle::pdf_document

    but instead

        output: pdf_document

    in the yaml header. I?m not quite sure why, but when BiocStyle is

used

    some of the latex code for code highlighting is repeated, leading to

the

    'already defined' error. I?ve not updated my package since before

this

    error started.

    BT

    > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com> a

?crit :

    >
    > Hey,
    >
    > I am trying to build my package Vegnette and I get the following

error:

    >
    > ! LaTeX Error: Command \VerbBar already defined.
    >               Or name \end... illegal, see p.192 of the manual.
    >
    > I tried to find what this means with no luck.
    >
    > Best,
    > Ioannis
    >
    >
    >    [[alternative HTML version deleted]]
    >
    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the helpers/macros.
Try this in a fresh interactive session:

  library(BiocStyle)
  rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue is and
thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit :

Thanks for the answer. However replacing it resulted in another error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

    I?ve been getting the exact same error for compiling the Rmarkdown
    vignettes in my own package. Some partial testing before the weekend
    revealed that in my case the error could be circumvented simply by

not

    using

        output: BiocStyle::pdf_document

    but instead

        output: pdf_document

    in the yaml header. I?m not quite sure why, but when BiocStyle is

used

    some of the latex code for code highlighting is repeated, leading

to the

    'already defined' error. I?ve not updated my package since before

this

    error started.

    BT

    > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com> a

?crit :

    >
    > Hey,
    >
    > I am trying to build my package Vegnette and I get the following

error:

    >
    > ! LaTeX Error: Command \VerbBar already defined.
    >               Or name \end... illegal, see p.192 of the manual.
    >
    > I tried to find what this means with no luck.
    >
    > Best,
    > Ioannis
    >
    >
    >    [[alternative HTML version deleted]]
    >
    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/bioc-devel

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to your
package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the helpers/macros.
Try this in a fresh interactive session:

  library(BiocStyle)
  rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue is and
thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit

:

Thanks for the answer. However replacing it resulted in another error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

    I?ve been getting the exact same error for compiling the Rmarkdown
    vignettes in my own package. Some partial testing before the

weekend

    revealed that in my case the error could be circumvented simply by

not

    using

        output: BiocStyle::pdf_document

    but instead

        output: pdf_document

    in the yaml header. I?m not quite sure why, but when BiocStyle is

used

    some of the latex code for code highlighting is repeated, leading

to the

    'already defined' error. I?ve not updated my package since before

this

    error started.

    BT

    > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com>

a ?crit :

    >
    > Hey,
    >
    > I am trying to build my package Vegnette and I get the following

error:

    >
    > ! LaTeX Error: Command \VerbBar already defined.
    >               Or name \end... illegal, see p.192 of the manual.
    >
    > I tried to find what this means with no luck.
    >
    > Best,
    > Ioannis
    >
    >
    >    [[alternative HTML version deleted]]
    >
    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/bioc-devel

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the development
and the release branch. The fix addresses vignette build errors occurring
with rmarkdown v1.18, these should clear up within the next build cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com> wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to your
package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the helpers/macros.
Try this in a fresh interactive session:

   library(BiocStyle)
   rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue is and
thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit

:

Thanks for the answer. However replacing it resulted in another error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

     I?ve been getting the exact same error for compiling the Rmarkdown
     vignettes in my own package. Some partial testing before the

weekend

     revealed that in my case the error could be circumvented simply by

not

     using

         output: BiocStyle::pdf_document

     but instead

         output: pdf_document

     in the yaml header. I?m not quite sure why, but when BiocStyle is

used

     some of the latex code for code highlighting is repeated, leading

to the

     'already defined' error. I?ve not updated my package since before

this

     error started.

     BT

     > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com>

a ?crit :

     >
     > Hey,
     >
     > I am trying to build my package Vegnette and I get the following

error:

     >
     > ! LaTeX Error: Command \VerbBar already defined.
     >               Or name \end... illegal, see p.192 of the manual.
     >
     > I tried to find what this means with no luck.
     >
     > Best,
     > Ioannis
     >
     >
     >    [[alternative HTML version deleted]]
     >
     > _______________________________________________
     > Bioc-devel at r-project.org mailing list
     > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k&s=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54&e=

	[[alternative HTML version deleted]]

Great news Andrzej! We'll keep a close eye on the build reports in the
next few days. Fingers crossed. Thanks!

H.


On 12/6/19 03:46, Andrzej Ole? wrote:

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the development
and the release branch. The fix addresses vignette build errors occurring
with rmarkdown v1.18, these should clear up within the next build cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com>

wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to

your

package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more

details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the

helpers/macros.

Try this in a fresh interactive session:

   library(BiocStyle)
   rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue is

and

thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a

?crit

:

Thanks for the answer. However replacing it resulted in another error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible ->

eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

     I?ve been getting the exact same error for compiling the

Rmarkdown

     vignettes in my own package. Some partial testing before the

weekend

     revealed that in my case the error could be circumvented simply

by

not

     using

         output: BiocStyle::pdf_document

     but instead

         output: pdf_document

     in the yaml header. I?m not quite sure why, but when BiocStyle

is

used

     some of the latex code for code highlighting is repeated,

leading

to the

     'already defined' error. I?ve not updated my package since

before

this

     error started.

     BT

     > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com

a ?crit :

     >
     > Hey,
     >
     > I am trying to build my package Vegnette and I get the

following

error:

     >
     > ! LaTeX Error: Command \VerbBar already defined.
     >               Or name \end... illegal, see p.192 of the

manual.

     >
     > I tried to find what this means with no luck.
     >
     > Best,
     > Ioannis
     >
     >
     >    [[alternative HTML version deleted]]
     >
     > _______________________________________________
     > Bioc-devel at r-project.org mailing list
     >

https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k&s=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54&e=

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      [[alternative HTML version deleted]]

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--
Herv? Pag?s

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: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

Hi all,
I've been following this conversation as I was having the same issue for
the swfdr package. Happy to see that it's now fixed on malbec and merida,
though I now see a different error on tokay, also referring to the
vignettes. I looked around a bit, and a bunch of other packages now have
the tokay error, which is:

* creating vignettes ... ERROR
--- re-building 'swfdrQ.Rmd' using rmarkdown
Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'swfdrQ.Rmd'


https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html


Thanks!
Cheers,
Simina



On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <hpages at fredhutch.org> wrote:

Great news Andrzej! We'll keep a close eye on the build reports in the
next few days. Fingers crossed. Thanks!

H.


On 12/6/19 03:46, Andrzej Ole? wrote:

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the

development

and the release branch. The fix addresses vignette build errors

occurring

with rmarkdown v1.18, these should clear up within the next build cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com>

wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to

your

package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more

details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the

helpers/macros.

Try this in a fresh interactive session:

   library(BiocStyle)
   rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue

is and

thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a

?crit

:

Thanks for the answer. However replacing it resulted in another

error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible ->

eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>;

Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with

BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

     I?ve been getting the exact same error for compiling the

Rmarkdown

     vignettes in my own package. Some partial testing before the

weekend

     revealed that in my case the error could be circumvented

simply by

not

     using

         output: BiocStyle::pdf_document

     but instead

         output: pdf_document

     in the yaml header. I?m not quite sure why, but when BiocStyle

is

used

     some of the latex code for code highlighting is repeated,

leading

to the

     'already defined' error. I?ve not updated my package since

before

this

     error started.

     BT

     > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <

iova89 at hotmail.com>

a ?crit :

     >
     > Hey,
     >
     > I am trying to build my package Vegnette and I get the

following

error:

     >
     > ! LaTeX Error: Command \VerbBar already defined.
     >               Or name \end... illegal, see p.192 of the

manual.

     >
     > I tried to find what this means with no luck.
     >
     > Best,
     > Ioannis
     >
     >
     >    [[alternative HTML version deleted]]
     >
     > _______________________________________________
     > Bioc-devel at r-project.org mailing list
     >

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--
Herv? Pag?s

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: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

Hi all,
I've been following this conversation as I was having the same issue for
the swfdr package. Happy to see that it's now fixed on malbec and merida,
though I now see a different error on tokay, also referring to the
vignettes. I looked around a bit, and a bunch of other packages now have
the tokay error, which is:

* creating vignettes ... ERROR
--- re-building 'swfdrQ.Rmd' using rmarkdown
Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'swfdrQ.Rmd'


https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html


Thanks!
Cheers,
Simina



On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <hpages at fredhutch.org> wrote:

Great news Andrzej! We'll keep a close eye on the build reports in the
next few days. Fingers crossed. Thanks!

H.


On 12/6/19 03:46, Andrzej Ole? wrote:

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the

development

and the release branch. The fix addresses vignette build errors

occurring

with rmarkdown v1.18, these should clear up within the next build cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com>

wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to

your

package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more

details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the

helpers/macros.

Try this in a fresh interactive session:

library(BiocStyle)
rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue

is and

thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a

?crit

:

Thanks for the answer. However replacing it resulted in another

error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible ->

eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>;

Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with

BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

I?ve been getting the exact same error for compiling the

Rmarkdown

vignettes in my own package. Some partial testing before the

weekend

revealed that in my case the error could be circumvented

simply by

not

using

output: BiocStyle::pdf_document

but instead

output: pdf_document

in the yaml header. I?m not quite sure why, but when BiocStyle

is

used

some of the latex code for code highlighting is repeated,

leading

to the

'already defined' error. I?ve not updated my package since

before

this

error started.

BT

Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <

iova89 at hotmail.com>

a ?crit :

Hey,

I am trying to build my package Vegnette and I get the

following

error:

! LaTeX Error: Command \VerbBar already defined.
Or name \end... illegal, see p.192 of the

manual.

I tried to find what this means with no luck.

Best,
Ioannis


[[alternative HTML version deleted]]

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--
Herv? Pag?s

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: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

Hi all,

I've also followed this thread as the FELLA package has problems with the
vignette as well.
I have two issues (link
<http://bioconductor.org/checkResults/devel/bioc-LATEST/FELLA/tokay2-buildsrc.html>
)
First:

Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "quickstart_files/figure-html/unnamed-chunk-12-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-12-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "quickstart_files/figure-html/unnamed-chunk-13-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-13-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "quickstart_files/figure-html/unnamed-chunk-14-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-14-1.png"' execution failed with error code 4
--- finished re-building 'quickstart.Rmd'

(but I believe this one does not prevent the vignette from building) And the second:

Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
argument is of length zero

This is the same one reported by Simina, in tokay2 too.

I hope the new adjustement fixes at least the second one.

Thank you Andrzej,
Sergi
??????

On Monday, December 09, 2019 11:37 CET, Andrzej Ole? <
andrzej.oles at gmail.com> wrote:


Hi Simina,

thank you for reporting the remaining problem on Windows builders. I have
just made an adjustment to BiocStyle which should resolve the issue.

Cheers,
Andrzej

On Sun, Dec 8, 2019 at 4:18 PM Simina Boca <smb310 at georgetown.edu> wrote:

Hi all,
I've been following this conversation as I was having the same issue for
the swfdr package. Happy to see that it's now fixed on malbec and merida,
though I now see a different error on tokay, also referring to the
vignettes. I looked around a bit, and a bunch of other packages now have
the tokay error, which is:

* creating vignettes ... ERROR
--- re-building 'swfdrQ.Rmd' using rmarkdown
Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'swfdrQ.Rmd'

https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html

Thanks!
Cheers,
Simina



On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <hpages at fredhutch.org>

wrote:

Great news Andrzej! We'll keep a close eye on the build reports in the
next few days. Fingers crossed. Thanks!

H.


On 12/6/19 03:46, Andrzej Ole? wrote:

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the

development

and the release branch. The fix addresses vignette build errors

occurring

with rmarkdown v1.18, these should clear up within the next build

cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com>

wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address

the

observed errors. Until then please refrain from making any changes to

your

package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com

wrote:

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more

details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the

helpers/macros.

Try this in a fresh interactive session:

library(BiocStyle)
rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the

issue

for passing R CMD check, but at least it?ll confirm what the issue

is and

thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a

?crit

:

Thanks for the answer. However replacing it resulted in another

error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible ->

eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>;

Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with

BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

I?ve been getting the exact same error for compiling the

Rmarkdown

vignettes in my own package. Some partial testing before the

weekend

revealed that in my case the error could be circumvented

simply by

not

using

output: BiocStyle::pdf_document

but instead

output: pdf_document

in the yaml header. I?m not quite sure why, but when BiocStyle

is

used

some of the latex code for code highlighting is repeated,

leading

to the

'already defined' error. I?ve not updated my package since

before

this

error started.

BT

Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <

iova89 at hotmail.com>

a ?crit :

Hey,

I am trying to build my package Vegnette and I get the

following

error:

! LaTeX Error: Command \VerbBar already defined.
Or name \end... illegal, see p.192 of the

manual.

I tried to find what this means with no luck.

Best,
Ioannis


[[alternative HTML version deleted]]

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--
Herv? Pag?s

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: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

[[alternative HTML version deleted]]

Great news Andrzej! We'll keep a close eye on the build reports in the 
next few days. Fingers crossed. Thanks!

H.


On 12/6/19 03:46, Andrzej Ole? wrote:

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the development
and the release branch. The fix addresses vignette build errors occurring
with rmarkdown v1.18, these should clear up within the next build cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com> 
wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to 
your
package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more 
details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the 
helpers/macros.
Try this in a fresh interactive session:

?? library(BiocStyle)
?? rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue 
is and
thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit

:

Thanks for the answer. However replacing it resulted in another error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> 
eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

???? I?ve been getting the exact same error for compiling the 
Rmarkdown
???? vignettes in my own package. Some partial testing before the

weekend

???? revealed that in my case the error could be circumvented 
simply by

not

???? using

???????? output: BiocStyle::pdf_document

???? but instead

???????? output: pdf_document

???? in the yaml header. I?m not quite sure why, but when 
BiocStyle is

used

???? some of the latex code for code highlighting is repeated, 
leading

to the

???? 'already defined' error. I?ve not updated my package since 
before

this

???? error started.

???? BT

???? > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com>

a ?crit :

???? >
???? > Hey,
???? >
???? > I am trying to build my package Vegnette and I get the 
following

error:

???? >
???? > ! LaTeX Error: Command \VerbBar already defined.
???? >?????????????? Or name \end... illegal, see p.192 of the 
manual.
???? >
???? > I tried to find what this means with no luck.
???? >
???? > Best,
???? > Ioannis
???? >
???? >
???? >??? [[alternative HTML version deleted]]
???? >
???? > _______________________________________________
???? > Bioc-devel at r-project.org mailing list
???? > 
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The tokay error is fixed now. Thank you all! Sergio, best wishes for
getting the other error fixed as well!

Cheers,
Simina

On Mon, Dec 9, 2019 at 5:25 PM Sergio Picart Armada <
sergi.picart at upc.edu

wrote:

Hi all,

I've also followed this thread as the FELLA package has problems with the
vignette as well.
I have two issues (link
<
http://bioconductor.org/checkResults/devel/bioc-LATEST/FELLA/tokay2-buildsrc.html

)
First:

Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "quickstart_files/figure-html/unnamed-chunk-12-1.png" -trim
"quickstart_files/figure-html/unnamed-chunk-12-1.png"' execution failed with
error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "quickstart_files/figure-html/unnamed-chunk-13-1.png" -trim
"quickstart_files/figure-html/unnamed-chunk-13-1.png"' execution failed with
error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "quickstart_files/figure-html/unnamed-chunk-14-1.png" -trim
"quickstart_files/figure-html/unnamed-chunk-14-1.png"' execution failed with
error code 4
--- finished re-building 'quickstart.Rmd'

(but I believe this one does not prevent the vignette from building) And the
second:

Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
argument is of length zero

This is the same one reported by Simina, in tokay2 too.

I hope the new adjustement fixes at least the second one.

Thank you Andrzej,
Sergi


On Monday, December 09, 2019 11:37 CET, Andrzej Ole? <
andrzej.oles at gmail.com

wrote:

Hi Simina,

thank you for reporting the remaining problem on Windows builders. I have
just made an adjustment to BiocStyle which should resolve the issue.

Cheers,
Andrzej

On Sun, Dec 8, 2019 at 4:18 PM Simina Boca <
smb310 at georgetown.edu

wrote:

Hi all,
I've been following this conversation as I was having the same issue for
the swfdr package. Happy to see that it's now fixed on malbec and merida,
though I now see a different error on tokay, also referring to the
vignettes. I looked around a bit, and a bunch of other packages now have
the tokay error, which is:

* creating vignettes ... ERROR
--- re-building 'swfdrQ.Rmd' using rmarkdown
Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'swfdrQ.Rmd'

https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html

Thanks!
Cheers,
Simina



On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <
hpages at fredhutch.org

wrote:

Great news Andrzej! We'll keep a close eye on the build reports in the
next few days. Fingers crossed. Thanks!

H.


On 12/6/19 03:46, Andrzej Ole? wrote:

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the

development

and the release branch. The fix addresses vignette build errors

occurring

with rmarkdown v1.18, these should clear up within the next build

cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <
andrzej.oles at gmail.com

wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address

the

observed errors. Until then please refrain from making any changes
to

your

package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <
andrzej.oles at gmail.com

wrote:

Hi,

the error seems to be related to some recent changes in the
upstream
package rmarkdown v1.18. I will give you an update once I know
more

details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca

wrote:

Not using BiocStyle::pdf_document means you can?t use the

helpers/macros.

Try this in a fresh interactive session:

library(BiocStyle)
rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the

issue

for passing R CMD check, but at least it?ll confirm what the
issue

is and

thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <
iova89 at hotmail.com

a

?crit

:

Thanks for the answer. However replacing it resulted in
another

error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible
->

eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <
mtmorgan.bioc at gmail.com

Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca

;

Ioannis

Vardaxis <
iova89 at hotmail.com

Kopi: 
bioc-devel at r-project.org
 <
bioc-devel at r-project.org

Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with

BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-
Marie

Tremblay" <
bioc-devel-bounces at r-project.org
 on behalf of
b2tremblay at uwaterloo.ca

wrote:
I?ve been getting the exact same error for compiling the

Rmarkdown

vignettes in my own package. Some partial testing before the

weekend

revealed that in my case the error could be circumvented

simply by

not

using

output: BiocStyle::pdf_document

but instead

output: pdf_document

in the yaml header. I?m not quite sure why, but when BiocStyle

is

used

some of the latex code for code highlighting is repeated,

leading

to the

'already defined' error. I?ve not updated my package since

before

this

error started.

BT

Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <

iova89 at hotmail.com

a ?crit :

Hey,

I am trying to build my package Vegnette and I get the

following

error:

! LaTeX Error: Command \VerbBar already defined.
Or name \end... illegal, see p.192 of the

manual.

I tried to find what this means with no luck.

Best,
Ioannis


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--
Herv? Pag?s

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: 
hpages at fredhutch.org

Phone: (206) 667-5791
Fax: (206) 667-1319

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

https://sites.google.com/georgetown.edu/siminaboca/

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