RNAseqData.HeLa.bam.chr14 0.1.6
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| Snapshot Date: 2014-01-06 07:15:21 -0800 (Mon, 06 Jan 2014) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RNAseqData.HeLa.bam.chr14 | | Last Changed Rev: 2646 / Revision: 2662 | | Last Changed Date: 2013-12-13 11:44:17 -0800 (Fri, 13 Dec 2013) |
| zin2 | Linux (Ubuntu 12.04.2 LTS) / x86_64 | OK | [ ERROR ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | ERROR | OK |
* using log directory ‘/home/biocbuild/bbs-2.14-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck’
* using R Under development (unstable) (2013-12-19 r64488)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAseqData.HeLa.bam.chr14/DESCRIPTION’ ... OK
* this is package ‘RNAseqData.HeLa.bam.chr14’ version ‘0.1.6’
* 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 ‘RNAseqData.HeLa.bam.chr14’ can be installed ... [1s/1s] WARNING
Found the following significant warnings:
Warning:
See ‘/home/biocbuild/bbs-2.14-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘RNAseqData.HNRNPC.bam.chr14’
A package should be listed in only one of these fields.
* 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 ... WARNING
Missing link or links in documentation object ‘RNAseqData.HeLa.bam.chr14-package.Rd’:
‘[GenomicRanges]{readGAlignmentPairs}’
See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
‘::’ or ‘:::’ import not declared from: ‘BiocInstaller’
‘library’ or ‘require’ call not declared from: ‘Rsamtools’
* checking examples ... ERROR
Running examples in ‘RNAseqData.HeLa.bam.chr14-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RNAseqData.HeLa.bam.chr14-package
> ### Title: Aligned reads from RNAseq experiment: Transcription profiling by
> ### high throughput sequencing of HNRNPC knockdown and control HeLa cells
> ### Aliases: RNAseqData.HeLa.bam.chr14-package RNAseqData.HeLa.bam.chr14
> ### RNAseqData.HeLa.bam.chr14_RUNNAMES RNAseqData.HeLa.bam.chr14_BAMFILES
> ### Keywords: package
>
> ### ** Examples
>
> RNAseqData.HeLa.bam.chr14_RUNNAMES
[1] "ERR127306" "ERR127307" "ERR127308" "ERR127309" "ERR127302" "ERR127303"
[7] "ERR127304" "ERR127305"
> RNAseqData.HeLa.bam.chr14_BAMFILES
ERR127306
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127306_chr14.bam"
ERR127307
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127307_chr14.bam"
ERR127308
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127308_chr14.bam"
ERR127309
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127309_chr14.bam"
ERR127302
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127302_chr14.bam"
ERR127303
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127303_chr14.bam"
ERR127304
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127304_chr14.bam"
ERR127305
"/home/biocbuild/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127305_chr14.bam"
>
> if (require(Rsamtools)) {
+ bamfiles <- RNAseqData.HeLa.bam.chr14_BAMFILES
+ param <- ScanBamParam(tag="NM")
+ if (BiocInstaller:::BIOC_VERSION >= 2.13)
+ func <- readGAlignmentPairs
+ else
+ func <- readGappedAlignmentPairs
+ galp <- func(bamfiles[1L], use.names=TRUE, param=param)
+ galp
+
+ first(galp) # 1st segment in each pair
+ last(galp) # 2nd segment in each pair
+
+ ## The alignments contain insertions, deletions, and gaps (I, D,
+ ## and N CIGAR operations, respectively):
+ colSums(cigarOpTable(cigar(first(galp))))
+ colSums(cigarOpTable(cigar(last(galp))))
+
+ ## ngap() returns the nb of gaps for each alignment:
+ table(ngap(first(galp)))
+ table(ngap(last(galp)))
+ table(ngap(first(galp)) + ngap(last(galp))) # up to 5 gaps per pair!
+
+ ## The NM tag gives the edit distance of each alignment to the
+ ## reference (ignoring the gaps):
+ table(mcols(first(galp))$NM)
+ table(mcols(last(galp))$NM)
+ table(mcols(first(galp))$NM + mcols(last(galp))$NM)
+ }
Loading required package: Rsamtools
Loading required package: IRanges
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 object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unlist
Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: Biostrings
Error: object 'readGAlignmentPairs' not found
Execution halted