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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gmapR
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* checking for file ‘gmapR/DESCRIPTION’ ... OK
* preparing ‘gmapR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gmapR.Rnw’ using Sweave
Loading required package: AnnotationDbi
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 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
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: IRanges
Loading required package: S4Vectors
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: GenomicFeatures
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: BiocIO
Loading required package: rtracklayer
Loading required package: Rsamtools
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//fa_coords -o ./TP53_demo_3.22.1.coords "/private/tmp/RtmpVP7Ifj/fileef982a5052"
Opening file /private/tmp/RtmpVP7Ifj/fileef982a5052
Contig TP53: concatenated at chromosome end: TP53:1..2025768 (length = 2025768 nt)
============================================================
Contig mapping information has been written to file ./TP53_demo_3.22.1.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
make gmapdb
============================================================
Running /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmap_process -c ./TP53_demo_3.22.1.coords "/private/tmp/RtmpVP7Ifj/fileef982a5052" | /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmapindex -d TP53_demo_3.22.1 -D . -A -s none
Reading coordinates from file ./TP53_demo_3.22.1.coords
Logging contig TP53 at TP53:1..2025768 in genome TP53_demo_3.22.1
Total genomic length = 2025768 bp
Chromosome TP53 has universal coordinates 1..2025768
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Running /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmap_process -c ./TP53_demo_3.22.1.coords "/private/tmp/RtmpVP7Ifj/fileef982a5052" | /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmapindex -d TP53_demo_3.22.1 -F . -D . -G
Genome length is 2025768 nt
Trying to allocate 189918*4 bytes of memory...succeeded. Building genome in memory.
Reading coordinates from file ./TP53_demo_3.22.1.coords
Writing contig TP53 to universal coordinates 1..2025768 in genome TP53_demo_3.22.1
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./TP53_demo_3.22.1.genomecomp | /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmapindex -d TP53_demo_3.22.1 -U > ./TP53_demo_3.22.1.genomebits
Running cat ./TP53_demo_3.22.1.genomecomp | /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d TP53_demo_3.22.1 -F . -D . -O
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome TP53_demo_3.22.1 (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 675253 k-mers...done
Running cat ./TP53_demo_3.22.1.genomecomp | /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d TP53_demo_3.22.1 -F . -D . -P
Looking for index files in directory . (offsets not compressed)
Offsets file is TP53_demo_3.22.1.ref123offsets
Positions file is TP53_demo_3.22.1.ref123positions
Trying to allocate 675253*4 bytes of memory...succeeded. Building positions in memory.
Indexing positions of oligomers in genome TP53_demo_3.22.1 (12 bp every 3 bp), position 0
Writing 675253 genomic positions to file ./TP53_demo_3.22.1.ref123positions ...
Running /private/tmp/RtmpsJSCcO/Rinstba9f4e2de682/gmapR/usr/bin//gmapindex -d TP53_demo_3.22.1 -F . -D . -S
SACA_K called with n = 2025769, K = 5, level 0
SACA_K called with n = 554308, K = 0, level 1
SACA_K called with n = 172586, K = 0, level 2
SACA_K called with n = 55408, K = 0, level 3
SACA_K called with n = 18042, K = 0, level 4
Computing lcp...done
Computing saindex...done
Copying files to directory /Users/biocbuild/.local/share/gmap/TP53_demo_3.22.1
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 18 out-of-bound ranges located on sequence chr17.
Note that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 18 out-of-bound ranges located on sequence chr17.
Note that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 20 out-of-bound ranges located on sequence TP53. Note
that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 18 out-of-bound ranges located on sequence TP53. Note
that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 14 out-of-bound ranges located on sequence TP53. Note
that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 18 out-of-bound ranges located on sequence TP53. Note
that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 14 out-of-bound ranges located on sequence TP53. Note
that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 32 out-of-bound ranges located on sequence TP53. Note
that ranges located on a sequence whose length is unknown (NA) or on a
circular sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
Error parsing TP53:-9550..-9549. Expecting coords (as <div>:<number>..<number>)
Problematic line was: >701792 TP53:-9550..-9549 donor 2
Error: processing vignette 'gmapR.Rnw' failed with diagnostics:
chunk 4 (label = set_TP53_splicesites)
Error in writeLines(lines, p) : ignoring SIGPIPE signal
--- failed re-building ‘gmapR.Rnw’
SUMMARY: processing the following file failed:
‘gmapR.Rnw’
Error: Vignette re-building failed.
Execution halted