This page was generated on 2023-05-26 06:18:13 -0000 (Fri, 26 May 2023).
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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 proBAMr
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* checking for file ‘proBAMr/DESCRIPTION’ ... OK
* preparing ‘proBAMr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘proBAMr.Rnw’ using Sweave
Loading required package: IRanges
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
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, aperm,
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
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: AnnotationDbi
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")'.
Build TranscriptDB object (txdb.sqlite) ...
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for
features of type stop_codon. This information was ignored.
OK
done
Prepare gene/transcript/protein id mapping information (ids.RData) ... done
Prepare exon annotation information (exon_anno.RData) ... done
Prepare protein sequence (proseq.RData) ... done
Prepare protein coding sequence (procodingseq.RData)... done
Error: processing vignette 'proBAMr.Rnw' failed with diagnostics:
unable to run pdflatex on 'proBAMr.tex'
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.10 ^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘proBAMr.Rnw’
SUMMARY: processing the following file failed:
‘proBAMr.Rnw’
Error: Vignette re-building failed.
Execution halted