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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 tRanslatome
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* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* preparing ‘tRanslatome’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
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, 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 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: GenomeInfoDb
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, dgamma, dnbinom, dnorm, dpois, dt, 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
Attaching package: ‘SparseM’
The following object is masked from ‘package:base’:
backsolve
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 v2.27.0 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
If you use GOSemSim in published research, please cite:
[36m-[39m 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. doi:10.1007/978-1-0716-0301-7_11
[36m-[39m Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978. doi:10.1093/bioinformatics/btq064
Loading required package: Heatplus
Loading required package: gplots
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
Building most specific GOs .....
( 1788 GO terms found. )
Build GO DAG topology ..........
( 1958 GO terms and 3225 relations. )
Annotating nodes ...............
( 19518 genes annotated to the GO terms. )
-- Elim Algorithm --
the algorithm is scoring 175 nontrivial nodes
parameters:
test statistic: fisher
cutOff: 0.01
Level 11: 3 nodes to be scored (0 eliminated genes)
Level 10: 7 nodes to be scored (0 eliminated genes)
Level 9: 13 nodes to be scored (0 eliminated genes)
Level 8: 21 nodes to be scored (23 eliminated genes)
Level 7: 30 nodes to be scored (28 eliminated genes)
Level 6: 33 nodes to be scored (3045 eliminated genes)
Level 5: 25 nodes to be scored (3334 eliminated genes)
Level 4: 20 nodes to be scored (3360 eliminated genes)
Level 3: 20 nodes to be scored (12743 eliminated genes)
Level 2: 2 nodes to be scored (12743 eliminated genes)
Level 1: 1 nodes to be scored (12743 eliminated genes)
Building most specific GOs .....
( 1788 GO terms found. )
Build GO DAG topology ..........
( 1958 GO terms and 3225 relations. )
Annotating nodes ...............
( 19518 genes annotated to the GO terms. )
-- Elim Algorithm --
the algorithm is scoring 180 nontrivial nodes
parameters:
test statistic: fisher
cutOff: 0.01
Level 12: 1 nodes to be scored (0 eliminated genes)
Level 11: 6 nodes to be scored (0 eliminated genes)
Level 10: 11 nodes to be scored (62 eliminated genes)
Level 9: 12 nodes to be scored (62 eliminated genes)
Level 8: 24 nodes to be scored (482 eliminated genes)
Level 7: 28 nodes to be scored (537 eliminated genes)
Level 6: 29 nodes to be scored (3055 eliminated genes)
Level 5: 24 nodes to be scored (3296 eliminated genes)
Level 4: 22 nodes to be scored (7505 eliminated genes)
Level 3: 20 nodes to be scored (7505 eliminated genes)
Level 2: 2 nodes to be scored (7505 eliminated genes)
Level 1: 1 nodes to be scored (7505 eliminated genes)
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...
Error: processing vignette 'tRanslatome_package.Rnw' failed with diagnostics:
unable to run pdflatex on 'tRanslatome_package.tex'
LaTeX errors:
! LaTeX Error: File `isorot.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.10 \usepackage
{epsfig}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘tRanslatome_package.Rnw’
SUMMARY: processing the following file failed:
‘tRanslatome_package.Rnw’
Error: Vignette re-building failed.
Execution halted