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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 tRanslatome
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* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* preparing ‘tRanslatome’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘tRanslatome_package.Rnw’ using Sweave
Loading required package: limma
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following object is masked from ‘package:limma’:
plotMA
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
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: IRanges
Loading required package: GenomicRanges
Loading required package: Seqinfo
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: 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: edgeR
Loading required package: RankProd
Loading required package: Rmpfr
Loading required package: gmp
Attaching package: ‘gmp’
The following objects are masked from ‘package:base’:
%*%, apply, crossprod, matrix, tcrossprod
C code of R package 'Rmpfr': GMP using 64 bits per limb
Attaching package: ‘Rmpfr’
The following object is masked from ‘package:gmp’:
outer
The following objects are masked from ‘package:SummarizedExperiment’:
cbind, rbind
The following objects are masked from ‘package:IRanges’:
cbind, pmax, pmin, rbind
The following objects are masked from ‘package:S4Vectors’:
cbind, rbind
The following objects are masked from ‘package:BiocGenerics’:
cbind, pmax, pmin, rbind
The following objects are masked from ‘package:stats’:
dbinom, dchisq, dgamma, dnbinom, dnorm, dpois, dt, pgamma, pnorm
The following objects are masked from ‘package:base’:
cbind, pmax, pmin, rbind
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: SparseM
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: ‘topGO’
The following object is masked from ‘package:IRanges’:
members
Loading required package: org.Hs.eg.db
Loading required package: GOSemSim
GOSemSim v2.39.0 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
Please cite:
Guangchuang Yu. Gene Ontology Semantic Similarity Analysis Using
GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks.
Methods in Molecular Biology. 2020, 2117:207-215. Humana, New York, NY.
Loading required package: Heatplus
Loading required package: gplots
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gplots 3.3.0 loaded:
* Use citation('gplots') for citation info.
* Homepage: https://talgalili.github.io/gplots/
* Report issues: https://github.com/talgalili/gplots/issues
* Ask questions: https://stackoverflow.com/questions/tagged/gplots
* Suppress this message with: suppressPackageStartupMessages(library(gplots))
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Attaching package: ‘gplots’
The following object is masked from ‘package:IRanges’:
space
The following object is masked from ‘package:S4Vectors’:
space
The following object is masked from ‘package:stats’:
lowess
Loading required package: plotrix
Attaching package: ‘plotrix’
The following object is masked from ‘package:gplots’:
plotCI
Error: processing vignette 'tRanslatome_package.Rnw' failed with diagnostics:
chunk 1
Error : unable to open database file
--- failed re-building ‘tRanslatome_package.Rnw’
SUMMARY: processing the following file failed:
‘tRanslatome_package.Rnw’
Error: Vignette re-building failed.
Execution halted