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### Running command:
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###   chmod a+r IgGeneUsage -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data IgGeneUsage
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* checking for file 'IgGeneUsage/DESCRIPTION' ... OK
* preparing 'IgGeneUsage':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'IgUsageCaseStudies.Rmd' using rmarkdown
Loading required package: IgGeneUsage
Loading required package: Rcpp
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: StanHeaders
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggforce
Loading required package: gridExtra

Attaching package: 'gridExtra'

The following object is masked from 'package:Biobase':

    combine

The following object is masked from 'package:BiocGenerics':

    combine

Loading required package: ggrepel
Loading required package: rstan
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
Loading required package: reshape2
Compiling model ... 

make cmd is
  make -f "C:/Users/BIOCBU~1/BBS-3~1.13-/R/etc/x64/Makeconf" -f "C:/Users/BIOCBU~1/BBS-3~1.13-/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="filede419d240e6.dll" WIN=64 TCLBIN=64 OBJECTS="filede419d240e6.o"

make would use
if test "zfilede419d240e6.o" != "z"; then \
  if test -e "filede419d240e6-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o filede419d240e6.dll filede419d240e6-win.def filede419d240e6.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o filede419d240e6.dll filede419d240e6-win.def filede419d240e6.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm filede419d240e6.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o filede419d240e6.dll tmp.def filede419d240e6.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o filede419d240e6.dll tmp.def filede419d240e6.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
Quitting from lines 223-231 (IgUsageCaseStudies.Rmd) 
Quitting from lines 223-231 (IgUsageCaseStudies.Rmd) 
Error: processing vignette 'IgUsageCaseStudies.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'IgUsageCaseStudies.Rmd'

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

Error: Vignette re-building failed.
Execution halted