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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data AnnotationForge
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* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* preparing ‘AnnotationForge’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MakingNewAnnotationPackages.Rnw’ using knitr
trying URL 'http://rest.uniprot.org/uniprotkb/search?query=P13368%20OR%20Q6GZX4&format=xml'
downloaded 45 KB

--- finished re-building ‘MakingNewAnnotationPackages.Rnw’

--- re-building ‘MakingNewOrganismPackages.Rmd’ using knitr
Warning in file.info(x, extra_cols = FALSE) :
  expanded path length 5574 would be too long for
<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Making New Organism Packages}
-->
<h1 id="making-organism-packages">Making Organism packages</h1>
<h3 id="by-marc-carlson">by Marc Carlson</h3>
<h2 id="overview">Overview</h2>
<p>Making Organism Packages is a straightforward process using the helper
functions makeOrgPackageFromNCBI() and makeOrgPackage().  If your
package is available at NCBI with an identifiable NCBI Taxonomy ID you
can try makeOrgPackageFromNCBI().  However, even if this fails, the
second and more general makeOrgPackage() function will allow you to
make a database package using only data.frames of data.</p>
<h2 id="making-use-of-makeorgpackagefromncbi">Making use of makeOrgPackageFromNCBI()</h2>
<p>The makeOrgPackageFromNCBI() function, will take several different
arguments to help declare who made the package and what species it is
for.  But the most important arguement is the tax_id arguement.  That
arguement is [... truncated]
--- finished re-building ‘MakingNewOrganismPackages.Rmd’

--- re-building ‘SQLForge.Rnw’ using knitr

Quitting from lines 177-193 [SQLForge] (SQLForge.Rnw)
Error: processing vignette 'SQLForge.Rnw' failed with diagnostics:
You must first install the human.db0 package!


--- failed re-building ‘SQLForge.Rnw’

--- re-building ‘makeProbePackage.Rnw’ using knitr

See
  ‘/tmp/Rtmpk8Wea1/hgu95av2probe.Rcheck/00check.log’
for details.


--- finished re-building ‘makeProbePackage.Rnw’

SUMMARY: processing the following file failed:
  ‘SQLForge.Rnw’

Error: Vignette re-building failed.
Execution halted