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### Running command:
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### chmod a+r GenomicRanges -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GenomicRanges
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* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* preparing 'GenomicRanges':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'GenomicRangesIntroduction.Rmd' using rmarkdown
Loading required package: stats4
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, 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
--- finished re-building 'GenomicRangesIntroduction.Rmd'
--- re-building 'ExtendingGenomicRanges.Rnw' using Sweave
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'ExtendingGenomicRanges.Rnw'
--- re-building 'GRanges_and_GRangesList_slides.Rnw' using Sweave
Warning in .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
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: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'GRanges_and_GRangesList_slides.Rnw'
--- re-building 'GenomicRangesHOWTOs.Rnw' using Sweave
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 exon. This information was ignored.
OK
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: 'AnnotationHub'
The following object is masked from 'package:Biobase':
cache
snapshotDate(): 2022-04-25
loading from cache
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:DESeq2':
plotMA
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: BSgenome
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:AnnotationHub':
hubUrl
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
The following object is masked from 'package:base':
plot
trying URL 'http://rest.kegg.jp/get/hsa05210/kgml'
downloaded 32 KB
Warning in download.file(kgml, destfile = destfile, method = method, ...) :
URL 'https://rest.kegg.jp/get/hsa05210/kgml': status was 'Failure when receiving data from the peer'
Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
chunk 53 (label = cancer_2)
Error in download.file(kgml, destfile = destfile, method = method, ...) :
download from 'http://rest.kegg.jp/get/hsa05210/kgml' failed
--- failed re-building 'GenomicRangesHOWTOs.Rnw'
--- re-building 'Ten_things_slides.Rnw' using Sweave
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'Ten_things_slides.Rnw'
SUMMARY: processing the following file failed:
'GenomicRangesHOWTOs.Rnw'
Error: Vignette re-building failed.
Execution halted
