GenomicRanges 1.24.3
Bioconductor Package Maintainer
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/GenomicRanges | | Last Changed Rev: 120819 / Revision: 122332 | | Last Changed Date: 2016-09-08 20:34:08 -0700 (Thu, 08 Sep 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.24.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.24.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicRanges’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'seqinfo' and siglist 'List'
generic 'seqinfo' and siglist 'RangedData'
generic 'seqinfo' and siglist 'RangesList'
generic 'seqinfo<-' and siglist 'List'
generic 'seqinfo<-' and siglist 'RangedData'
generic 'seqnames' and siglist 'RangedData'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘GRanges_and_GRangesList_slides.pdf’ from 459Kb to 240Kb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicRanges-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeGRangesFromDataFrame
> ### Title: Make a GRanges object from a data.frame or DataFrame
> ### Aliases: makeGRangesFromDataFrame coerce,data.frame,GRanges-method
> ### coerce,DataFrame,GRanges-method
> ### Keywords: manip
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## BASIC EXAMPLES
> ## ---------------------------------------------------------------------
>
> df <- data.frame(chr="chr1", start=11:15, end=12:16,
+ strand=c("+","-","+","*","."), score=1:5)
> df
chr start end strand score
1 chr1 11 12 + 1
2 chr1 12 13 - 2
3 chr1 13 14 + 3
4 chr1 14 15 * 4
5 chr1 15 16 . 5
> makeGRangesFromDataFrame(df) # strand value "." is replaced with "*"
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] +
[2] chr1 [12, 13] -
[3] chr1 [13, 14] +
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> ## The strand column is optional:
> df <- data.frame(chr="chr1", start=11:15, end=12:16, score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] *
[2] chr1 [12, 13] *
[3] chr1 [13, 14] *
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> gr <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)
> gr2 <- as(df, "GRanges") # equivalent to the above
> stopifnot(identical(gr, gr2))
> gr2 <- GRanges(df) # equivalent to the above
> stopifnot(identical(gr, gr2))
>
> makeGRangesFromDataFrame(df, ignore.strand=TRUE)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] *
[2] chr1 [12, 13] *
[3] chr1 [13, 14] *
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
+ ignore.strand=TRUE)
GRanges object with 5 ranges and 1 metadata column:
seqnames ranges strand | score
<Rle> <IRanges> <Rle> | <integer>
[1] chr1 [11, 12] * | 1
[2] chr1 [12, 13] * | 2
[3] chr1 [13, 14] * | 3
[4] chr1 [14, 15] * | 4
[5] chr1 [15, 16] * | 5
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> makeGRangesFromDataFrame(df, seqinfo=paste0("chr", 4:1))
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] *
[2] chr1 [12, 13] *
[3] chr1 [13, 14] *
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
> makeGRangesFromDataFrame(df, seqinfo=c(chrM=NA, chr1=500, chrX=100))
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] *
[2] chr1 [12, 13] *
[3] chr1 [13, 14] *
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 3 sequences from an unspecified genome
> makeGRangesFromDataFrame(df, seqinfo=Seqinfo(paste0("chr", 4:1)))
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] *
[2] chr1 [12, 13] *
[3] chr1 [13, 14] *
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
>
> ## ---------------------------------------------------------------------
> ## ABOUT AUTOMATIC DETECTION OF THE seqnames/start/end/strand COLUMNS
> ## ---------------------------------------------------------------------
>
> ## Automatic detection of the seqnames/start/end/strand columns is
> ## case insensitive:
> df <- data.frame(ChRoM="chr1", StarT=11:15, stoP=12:16,
+ STRAND=c("+","-","+","*","."), score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] +
[2] chr1 [12, 13] -
[3] chr1 [13, 14] +
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> ## It also ignores a common prefix between the start and end columns:
> df <- data.frame(seqnames="chr1", tx_start=11:15, tx_end=12:16,
+ strand=c("+","-","+","*","."), score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [11, 12] +
[2] chr1 [12, 13] -
[3] chr1 [13, 14] +
[4] chr1 [14, 15] *
[5] chr1 [15, 16] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> ## The common prefix between the start and end columns is used to
> ## disambiguate between more than one seqnames column:
> df <- data.frame(chrom="chr1", tx_start=11:15, tx_end=12:16,
+ tx_chr="chr2", score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 [11, 12] *
[2] chr2 [12, 13] *
[3] chr2 [13, 14] *
[4] chr2 [14, 15] *
[5] chr2 [15, 16] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> ## ---------------------------------------------------------------------
> ## 0-BASED VS 1-BASED START POSITIONS
> ## ---------------------------------------------------------------------
>
> if (require(rtracklayer)) {
+ session <- browserSession()
+ genome(session) <- "sacCer2"
+ query <- ucscTableQuery(session, "Most Conserved")
+ df <- getTable(query)
+
+ ## A common pitfall is to forget that the UCSC Table Browser uses the
+ ## "0-based start" convention:
+ gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)
+ head(gr0)
+ min(start(gr0))
+
+ ## The start positions need to be converted into 1-based positions,
+ ## to adhere to the convention used in Bioconductor:
+ gr1 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
+ starts.in.df.are.0based=TRUE)
+ head(gr1)
+ }
Loading required package: rtracklayer
Error in `genome<-`(`*tmp*`, value = "sacCer2") :
Failed to set session genome to 'sacCer2'
Calls: genome<- -> genome<-
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.