This page was generated on 2019-10-16 12:47:44 -0400 (Wed, 16 Oct 2019).
GenomicFeatures 1.36.4 Bioconductor Package Maintainer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
URL: https://git.bioconductor.org/packages/GenomicFeatures |
Branch: RELEASE_3_9 |
Last Commit: 28082ec |
Last Changed Date: 2019-07-09 04:52:32 -0400 (Tue, 09 Jul 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
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, 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, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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")'.
[1] TRUE
> GenomicFeatures:::.test()
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: rtracklayer
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
RUNIT TEST PROTOCOL -- Wed Oct 16 03:29:27 2019
***********************************************
Number of test functions: 75
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75
Number of errors: 0
Number of failures: 0
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 3 out-of-bound ranges located on sequences a,
b, and c. 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.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence c.
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.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence c.
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.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 4 out-of-bound ranges located on sequences 1,
2, 3, and 4. 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.
5: 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.
6: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
7: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
>
> proc.time()
user system elapsed
208.036 5.528 231.647