Re: [Bioc-devel] bioctitle issue for Rmd

[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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QQEy7hX7LwNRfF2vOZqRi_8FzxYRlsfwkrE-ikutFo8&s=DK8vF4FSB0aOHaOmdcHCs_2qILx4O70kCr3gdn2oWyg&e=
>   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] Question regarding pruning release of large files

[Saskia Freytag]

Hi,

I stupidly added and tracked some large files in my package repo at the start. 
I have since deleted these files and would like to permanently remove them form 
my GitHub history. I have been able to this locally. However when I try to do 
‘git push upstream RELEASE_3_10’, it asks me to fetch first. This results in 
the history being restored. I have tried to do ‘git push —force’, but this 
results in an error. Is there any way to delete the history of these files from 
the upstream?

Cheers,

Saskia
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