subject:"\[Bioc\-devel\] bioctitle issue for Rmd"

Re: [Bioc-devel] bioctitle issue for Rmd

2019-12-20 Thread Sergio Picart Armada



Hi all, 

Also experiencing this. 
http://bioconductor.org/checkResults/release/bioc-LATEST/FELLA/tokay1-buildsrc.html

Hope it gets fixed soon,
S

On Wednesday, December 18, 2019 11:30 CET, "Pages, Herve" 
 wrote:
 Hi Vince,

I opened an issue on GitHub for this:

https://github.com/Bioconductor/BiocStyle/issues/68

H.

On 12/15/19 14:31, Vincent Carey wrote:
> On my mac and linux systems I am seeing a new
>
> error. With the latest checkout of BiocStyle
>
>
> rmarkdown::render("foo/BiocStyle/vignettes/AuthoringRmdVignettes.Rmd",
> BiocStyle::pdf_document())
>
>
> produced
>
>
> ! Undefined control sequence.
>
> l.56 \bioctitle
>
> []{Authoring R Markdown vignettes}
>
>
> Error: Failed to compile AuthoringRmdVignettes.tex. See
> https://urldefense.proofpoint.com/v2/url?u=https-3A__yihui.org_tinytex_r_-23debugging=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=QQEy7hX7LwNRfF2vOZqRi_8FzxYRlsfwkrE-ikutFo8=DK8vF4FSB0aOHaOmdcHCs_2qILx4O70kCr3gdn2oWyg=
>  for debugging tips. See
> AuthoringRmdVignettes.log for more info.
>
>> sessionInfo()
>
> R Under development (unstable) (2019-12-06 r77536)
>
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> Running under: Debian GNU/Linux 10 (buster)
>
>
> Matrix products: default
>
> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
>
>
> locale:
>
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
>
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
>
> other attached packages:
>
> [1] BiocStyle_2.15.2 rmarkdown_2.0 BiocManager_1.30.10
>
>
> loaded via a namespace (and not attached):
>
> [1] Rcpp_1.0.3 bookdown_0.16 digest_0.6.23 magrittr_1.5
>
> [5] evaluate_0.14 rlang_0.4.2 stringi_1.4.3 tools_4.0.0
>
> [9] stringr_1.4.0 tinytex_0.18 xfun_0.11 yaml_2.2.0
>
> [13] compiler_4.0.0 htmltools_0.4.0 knitr_1.26
>

--
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
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Re: [Bioc-devel] bioctitle issue for Rmd

2019-12-18 Thread Pages, Herve

Hi Vince,

I opened an issue on GitHub for this:

   https://github.com/Bioconductor/BiocStyle/issues/68

H.

On 12/15/19 14:31, Vincent Carey wrote:
> On my mac and linux systems I am seeing a new
> 
> error.  With the latest checkout of BiocStyle
> 
> 
> rmarkdown::render("foo/BiocStyle/vignettes/AuthoringRmdVignettes.Rmd",
> BiocStyle::pdf_document())
> 
> 
> produced
> 
> 
> ! Undefined control sequence.
> 
> l.56 \bioctitle
> 
> []{Authoring R Markdown vignettes}
> 
> 
> Error: Failed to compile AuthoringRmdVignettes.tex. See
> https://urldefense.proofpoint.com/v2/url?u=https-3A__yihui.org_tinytex_r_-23debugging=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=QQEy7hX7LwNRfF2vOZqRi_8FzxYRlsfwkrE-ikutFo8=DK8vF4FSB0aOHaOmdcHCs_2qILx4O70kCr3gdn2oWyg=
>   for debugging tips. See
> AuthoringRmdVignettes.log for more info.
> 
>> sessionInfo()
> 
> R Under development (unstable) (2019-12-06 r77536)
> 
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> Running under: Debian GNU/Linux 10 (buster)
> 
> 
> Matrix products: default
> 
> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
> 
> 
> locale:
> 
>   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> 
>   [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> 
>   [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=C
> 
>   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> 
>   [9] LC_ADDRESS=C   LC_TELEPHONE=C
> 
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> 
> attached base packages:
> 
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> 
> other attached packages:
> 
> [1] BiocStyle_2.15.2rmarkdown_2.0   BiocManager_1.30.10
> 
> 
> loaded via a namespace (and not attached):
> 
>   [1] Rcpp_1.0.3  bookdown_0.16   digest_0.6.23   magrittr_1.5
> 
>   [5] evaluate_0.14   rlang_0.4.2 stringi_1.4.3   tools_4.0.0
> 
>   [9] stringr_1.4.0   tinytex_0.18xfun_0.11   yaml_2.2.0
> 
> [13] compiler_4.0.0  htmltools_0.4.0 knitr_1.26
> 

-- 
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
___
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[Bioc-devel] bioctitle issue for Rmd

2019-12-15 Thread Vincent Carey

On my mac and linux systems I am seeing a new

error.  With the latest checkout of BiocStyle


rmarkdown::render("foo/BiocStyle/vignettes/AuthoringRmdVignettes.Rmd",
BiocStyle::pdf_document())


produced


! Undefined control sequence.

l.56 \bioctitle

   []{Authoring R Markdown vignettes}


Error: Failed to compile AuthoringRmdVignettes.tex. See
https://yihui.org/tinytex/r/#debugging for debugging tips. See
AuthoringRmdVignettes.log for more info.

> sessionInfo()

R Under development (unstable) (2019-12-06 r77536)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Debian GNU/Linux 10 (buster)


Matrix products: default

BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so


locale:

 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=C

 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C

 [9] LC_ADDRESS=C   LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C


attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base


other attached packages:

[1] BiocStyle_2.15.2rmarkdown_2.0   BiocManager_1.30.10


loaded via a namespace (and not attached):

 [1] Rcpp_1.0.3  bookdown_0.16   digest_0.6.23   magrittr_1.5

 [5] evaluate_0.14   rlang_0.4.2 stringi_1.4.3   tools_4.0.0

 [9] stringr_1.4.0   tinytex_0.18xfun_0.11   yaml_2.2.0

[13] compiler_4.0.0  htmltools_0.4.0 knitr_1.26

-- 
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Re: [Bioc-devel] bioctitle issue for Rmd

Re: [Bioc-devel] bioctitle issue for Rmd

[Bioc-devel] bioctitle issue for Rmd

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