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I'm generating a README.md GitHub page from a Rmd file. It was generated correctly a week ago but now it's throwing the following error:

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS README.md --to html --from markdown_github --output README.html --standalone --self-contained --highlight-style pygments --template "C:\Users\E\Documents\R\win-library\3.3\rmarkdown\rmarkdown\templates\github_document\resources\preview.html" --variable "github-markdown-css:C:\Users\E\Documents\R\win-library\3.3\rmarkdown\rmarkdown\templates\github_document\resources\github.css" --email-obfuscation none pandoc.exe: Could not fetch https://img.shields.io/codecov/c/github/erzk/fnirsr/master.svg HttpExceptionRequest Request { host = "img.shields.io" port = 443 secure = True requestHeaders = [] path = "/codecov/c/github/erzk/fnirsr/master.svg" queryString = "" method = "GET" proxy = Nothing
rawBody = False redirectCount = 10
responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 } (InternalException (HandshakeFailed Error_EOF)) Error: pandoc document conversion failed with error 67 In addition: Warning message: running command '"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS README.md --to html --from markdown_github --output README.html --standalone --self-contained --highlight-style pygments --template "C:\Users\E\Documents\R\win-library\3.3\rmarkdown\rmarkdown\templates\github_document\resources\preview.html" --variable "github-markdown-css:C:\Users\E\Documents\R\win-library\3.3\rmarkdown\rmarkdown\templates\github_document\resources\github.css" --email-obfuscation none' had status 67 Execution halted

I checked the URL and it works, the badge is also visible on the old README.md file.

As suggested here, I updated rmarkdown and knitr (first to CRAN version, then to GitHub version), but it didn't help.

Then I tried adding self_contained: no as suggested here. Still throws an error.

sessionInfo()

R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: 1 LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 4 LC_NUMERIC=C
LC_TIME=English_United Kingdom.1252

attached base packages: 1 stats graphics grDevices utils
datasets methods base

other attached packages: 1 fnirsr_0.1.0

loaded via a namespace (and not attached): 1 Rcpp_0.12.8
knitr_1.16.3 magrittr_1.5 lattice_0.20-34 R6_2.2.0
stringr_1.2.0 [7] dplyr_0.5.0 tools_3.3.2
grid_3.3.2 R.oo_1.21.0 RPMG_2.2-1 DBI_0.5-1
[13] R.matlab_3.6.1 htmltools_0.3.6 yaml_2.1.14
assertthat_0.1 digest_0.6.12 rprojroot_1.2 [19] tibble_1.2 readr_1.0.0 R.utils_2.5.0 evaluate_0.10 rmarkdown_1.5.9000 stringi_1.1.2 [25] RSEIS_3.7-4
backports_1.0.4 R.methodsS3_1.7.1 Rwave_2.4-5 zoo_1.7-14

I get the same error on Ubuntu 16.04.

I didn't submit it as an issue to knitr yet as there might be a simple solution.

Any ideas how to fix it?

epo3
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    It compiles fine on my machine. Are you maybe behind a proxy or have another network specificity to prevents rstudio from connecting to that url? – scoa May 23 '17 at 09:16
  • I use a VPN, but it doesn't seem to be the reason for the error. I turned it off and still got the same error. I was still using a VPN last time when the Rmd compiled. I also tried disabling my malware protection software. That didn't help either. – epo3 May 23 '17 at 18:36
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    a related question from today with the same ` (InternalException (HandshakeFailed Error_EOF))`: https://stackoverflow.com/questions/44136481/render-code-for-google-chart-in-rmarkdown-rmd – scoa May 23 '17 at 20:16
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    see my answer on the question scoa linked to... – mb21 May 24 '17 at 03:55
  • @mb21 your solution worked for me. for some reason the html generated locally is still missing the shield but it looks fine when uploaded to GitHub. feel free to post your answer here so that I can accept it. – epo3 May 24 '17 at 20:09

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