Error(s) in re-building vignettes:
--- re-building 'Develop_and_Use_the_dmdScheme.Rmd' using rmarkdown

#############################################
The cache will be in a temporary location and be deleted when you quit R.
It is located at
   D:\temp\Rtmp8uheGC\dmdScheme_15d102e2172f1
To make it permanent, call
   cache(createPermanent = TRUE)
and restart R
and a permanent cache will be created which will survive restarts.
#############################################


trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/dmdScheme_0.9.9.tar.gz'
Content type 'application/octet-stream' length 39383 bytes (38 KB)
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downloaded 38 KB

Scheme definition `D:\temp\Rtmp8uheGC\file15d1061d46464/dmdScheme_0.9.9.tar.gz, installed with
name:    dmdScheme
version: 0.9.9
Theme switched to dmdScheme_0.9.9
trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/SCHEME_DEFINITIONS.yaml'
Content type 'text/plain; charset=utf-8' length 478 bytes
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downloaded 478 bytes

trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/emeScheme_0.9.5.tar.gz'
Content type 'application/octet-stream' length 129249 bytes (126 KB)
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downloaded 126 KB

trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/emeScheme_0.9.5.tar.gz'
Content type 'application/octet-stream' length 129249 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/triebeard_0.3.0.zip'
Content type 'application/zip' length 726595 bytes (709 KB)
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downloaded 709 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/XML_3.99-0.3.zip'
Content type 'application/zip' length 4255589 bytes (4.1 MB)
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downloaded 4.1 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/WikipediR_1.5.0.zip'
Content type 'application/zip' length 83285 bytes (81 KB)
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downloaded 81 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/urltools_1.7.3.zip'
Content type 'application/zip' length 870618 bytes (850 KB)
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downloaded 850 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/httpcode_0.3.0.zip'
Content type 'application/zip' length 35002 bytes (34 KB)
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downloaded 34 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/iterators_1.0.12.zip'
Content type 'application/zip' length 343925 bytes (335 KB)
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downloaded 335 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/reshape_0.8.8.zip'
Content type 'application/zip' length 171229 bytes (167 KB)
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downloaded 167 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/plyr_1.8.6.zip'
Content type 'application/zip' length 1310998 bytes (1.3 MB)
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downloaded 1.3 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/rentrez_1.2.2.zip'
Content type 'application/zip' length 141126 bytes (137 KB)
==================================================
downloaded 137 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/rncl_0.8.4.zip'
Content type 'application/zip' length 1515322 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/solrium_1.1.4.zip'
Content type 'application/zip' length 426888 bytes (416 KB)
==================================================
downloaded 416 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/WikidataR_1.4.0.zip'
Content type 'application/zip' length 56756 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/quadprog_1.5-8.zip'
Content type 'application/zip' length 54859 bytes (53 KB)
==================================================
downloaded 53 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/igraph_1.2.5.zip'
Content type 'application/zip' length 9165651 bytes (8.7 MB)
=================================================
downloaded 8.6 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/fastmatch_1.1-0.zip'
Content type 'application/zip' length 53811 bytes (52 KB)
==================================================
downloaded 52 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/crul_0.9.0.zip'
Content type 'application/zip' length 403638 bytes (394 KB)
==================================================
downloaded 394 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/foreach_1.5.0.zip'
Content type 'application/zip' length 145920 bytes (142 KB)
==================================================
downloaded 142 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/ape_5.4.zip'
Content type 'application/zip' length 2858524 bytes (2.7 MB)
==============================================
downloaded 2.6 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/zoo_1.8-8.zip'
Content type 'application/zip' length 1096019 bytes (1.0 MB)
========================================
downloaded 876 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/data.table_1.12.8.zip'
Content type 'application/zip' length 2276767 bytes (2.2 MB)
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downloaded 2.2 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/bold_1.1.0.zip'
Content type 'application/zip' length 106353 bytes (103 KB)
==================================================
downloaded 103 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/rredlist_0.6.0.zip'
Content type 'application/zip' length 85734 bytes (83 KB)
==================================================
downloaded 83 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/rotl_3.0.10.zip'
Content type 'application/zip' length 472845 bytes (461 KB)
==================================================
downloaded 461 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/ritis_0.9.0.zip'
Content type 'application/zip' length 161341 bytes (157 KB)
==================================================
downloaded 157 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/worrms_0.4.0.zip'
Content type 'application/zip' length 103252 bytes (100 KB)
==================================================
downloaded 100 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/natserv_1.0.0.zip'
Content type 'application/zip' length 150930 bytes (147 KB)
==================================================
downloaded 147 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/wikitaxa_0.3.0.zip'
Content type 'application/zip' length 436279 bytes (426 KB)
==================================================
downloaded 426 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/phangorn_2.5.5.zip'
Content type 'application/zip' length 2950055 bytes (2.8 MB)
===============================================
downloaded 2.7 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/conditionz_0.1.0.zip'
Content type 'application/zip' length 57351 bytes (56 KB)
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downloaded 56 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/taxize_0.9.97.zip'
Content type 'application/zip' length 1550840 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

Quitting from lines 206-207 (Develop_and_Use_the_dmdScheme.Rmd) 
Error: processing vignette 'Develop_and_Use_the_dmdScheme.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'Develop_and_Use_the_dmdScheme.Rmd'

SUMMARY: processing the following file failed:
  'Develop_and_Use_the_dmdScheme.Rmd'

Error: Vignette re-building failed.
Execution halted