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\RtmpGIKhCS\dmdScheme_27574616f42cf
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\RtmpGIKhCS\file27574d182b6a/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
==================================================
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)
==================================================
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/4.1/triebeard_0.3.0.zip'
Content type 'application/zip' length 932814 bytes (910 KB)
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downloaded 910 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/XML_3.99-0.3.zip'
Content type 'application/zip' length 4260808 bytes (4.1 MB)
================================================
downloaded 3.9 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/WikipediR_1.5.0.zip'
Content type 'application/zip' length 83267 bytes (81 KB)
==================================================
downloaded 81 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/urltools_1.7.3.zip'
Content type 'application/zip' length 1072470 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/httpcode_0.3.0.zip'
Content type 'application/zip' length 34979 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/iterators_1.0.12.zip'
Content type 'application/zip' length 343862 bytes (335 KB)
==================================================
downloaded 335 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/reshape_0.8.8.zip'
Content type 'application/zip' length 170187 bytes (166 KB)
==================================================
downloaded 166 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/plyr_1.8.6.zip'
Content type 'application/zip' length 1496864 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/rentrez_1.2.2.zip'
Content type 'application/zip' length 140982 bytes (137 KB)
==================================================
downloaded 137 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/rncl_0.8.4.zip'
Content type 'application/zip' length 1687648 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/solrium_1.1.4.zip'
Content type 'application/zip' length 426724 bytes (416 KB)
==================================================
downloaded 416 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/WikidataR_1.4.0.zip'
Content type 'application/zip' length 56864 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/quadprog_1.5-8.zip'
Content type 'application/zip' length 50249 bytes (49 KB)
==================================================
downloaded 49 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/igraph_1.2.5.zip'
Content type 'application/zip' length 9340658 bytes (8.9 MB)
=================================================
downloaded 8.7 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/fastmatch_1.1-0.zip'
Content type 'application/zip' length 53047 bytes (51 KB)
==================================================
downloaded 51 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/crul_0.9.0.zip'
Content type 'application/zip' length 402093 bytes (392 KB)
==================================================
downloaded 392 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/foreach_1.5.0.zip'
Content type 'application/zip' length 146056 bytes (142 KB)
==================================================
downloaded 142 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/ape_5.4.zip'
Content type 'application/zip' length 3008242 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/zoo_1.8-8.zip'
Content type 'application/zip' length 1095669 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/bold_1.0.0.zip'
Content type 'application/zip' length 106640 bytes (104 KB)
==================================================
downloaded 104 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/rredlist_0.6.0.zip'
Content type 'application/zip' length 85214 bytes (83 KB)
==================================================
downloaded 83 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/rotl_3.0.10.zip'
Content type 'application/zip' length 473563 bytes (462 KB)
==================================================
downloaded 462 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/ritis_0.9.0.zip'
Content type 'application/zip' length 161546 bytes (157 KB)
==================================================
downloaded 157 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/worrms_0.4.0.zip'
Content type 'application/zip' length 103296 bytes (100 KB)
==================================================
downloaded 100 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/natserv_1.0.0.zip'
Content type 'application/zip' length 150889 bytes (147 KB)
==================================================
downloaded 147 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/wikitaxa_0.3.0.zip'
Content type 'application/zip' length 436008 bytes (425 KB)
==================================================
downloaded 425 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/phangorn_2.5.5.zip'
Content type 'application/zip' length 3128589 bytes (3.0 MB)
==============================================
downloaded 2.8 MB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/conditionz_0.1.0.zip'
Content type 'application/zip' length 57528 bytes (56 KB)
==================================================
downloaded 56 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.1/taxize_0.9.97.zip'
Content type 'application/zip' length 1550029 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