ggbio 1.31.2
Michael Lawrence
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ggbio |
| Branch: master |
| Last Commit: a36c7b4 |
| Last Changed Date: 2019-03-19 13:36:35 -0400 (Tue, 19 Mar 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### chmod a+r ggbio -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ggbio
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* checking for file 'ggbio/DESCRIPTION' ... OK
* preparing 'ggbio':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'ggbio.Rnw' using Sweave
--- finished re-building 'ggbio.Rnw'
cp realvignettes/*.Rnw .
C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "library(knitr); knit2pdf('ggbio.Rnw')"
processing file: ggbio.Rnw
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$ results: chr "asis"
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$ include: logi FALSE
$ cache : logi FALSE
$ eval : logi TRUE
$ echo : logi FALSE
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$ fig.width : num 5.5
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Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: ggplot2
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
use chr1 automatically
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
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windows
Loading required package: GenomeInfoDb
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `./figures/ggbio-unnamed-chunk-4-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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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")'.
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
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aggregating...
Done
'select()' returned 1:1 mapping between keys and columns
Constructing graphics...
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
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aggregating...
Done
'select()' returned 1:1 mapping between keys and columns
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `./figures/ggbio-unnamed-chunk-5-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Parsing transcripts...
Parsing exons...
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Parsing utrs...
------exons...
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aggregating...
Done
'select()' returned 1:1 mapping between keys and columns
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Parsing transcripts...
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Parsing utrs...
------exons...
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aggregating...
Done
'select()' returned 1:1 mapping between keys and columns
Constructing graphics...
reduce alignemnts...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Parsing transcripts...
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------exons...
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aggregating...
Done
'select()' returned 1:many mapping between keys and columns
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Parsing transcripts...
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aggregating...
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Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Loading required package: ensembldb
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
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Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Parsing transcripts...
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Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Loading required package: BSgenome
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Attaching package: 'Biostrings'
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Loading required package: rtracklayer
Scale for 'y' is already present. Adding another scale for 'y', which will
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Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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reading in as Bamfile
Parsing raw coverage...
Read GAlignments from BamFile...
extracting information...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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reading in as Bamfile
Read GAlignments from BamFile...
plotting...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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reading in as Bamfile
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reading in as Bamfile
Estimating coverage...
Constructing graphics...
reading in as Bamfile
Estimating coverage...
Constructing graphics...
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
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Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
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Loading required package: BiocParallel
Attaching package: 'DelayedArray'
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Loading required package: Rsamtools
Attaching package: 'VariantAnnotation'
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Quitting from lines 374-388 (ggbio.Rnw)
Error: scanVcf: missing value where TRUE/FALSE needed
path: C:/Users/biocbuild/bbs-3.9-bioc/R/library/biovizBase/extdata/17-1409-CEU-brca1.vcf.bgz
In addition: Warning messages:
1: `panel.margin` is deprecated. Please use `panel.spacing` property instead
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead
4: `panel.margin` is deprecated. Please use `panel.spacing` property instead
5: Removed 2 rows containing missing values (geom_text).
6: Removed 2 rows containing missing values (geom_text).
7: Removed 2 rows containing missing values (geom_text).
8: Removed 1 rows containing missing values (geom_text).
9: Removed 6 rows containing missing values (geom_text).
10: 'GenenameFilter' is deprecated.
Use 'GeneNameFilter' instead.
See help("Deprecated")
Execution halted
make: *** [ggbio.pdf] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted