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### Running command:
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###   chmod a+r InterMineR -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data InterMineR
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* checking for file 'InterMineR/DESCRIPTION' ... OK
* preparing 'InterMineR':
* checking DESCRIPTION meta-information ... OK
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
Warning: D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpqyE56x/Rbuild2bd0274c3299/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'InterMineR.Rmd' using rmarkdown
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'subtract'
Warning: multiple methods tables found for 'intersect'

Attaching package: 'InterMineR'

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

    intersect, union

Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    intersect, union

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


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: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'GenomicRanges'

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

    subtract

Loading required package: grid
Quitting from lines 477-491 (InterMineR.Rmd) 
Error: processing vignette 'InterMineR.Rmd' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building 'InterMineR.Rmd'

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

Error: Vignette re-building failed.
Execution halted