RIPSeeker 1.11.0
Yue Li
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RIPSeeker | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | 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 RIPSeeker_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RIPSeeker.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RIPSeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RIPSeeker’ version ‘1.11.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Rsamtools’
‘GenomicAlignments’ ‘rtracklayer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘RIPSeeker’ can be installed ... [13s/13s] 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 ... NOTE
'library' or 'require' call to ‘Rsamtools’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘ChIPpeakAnno’ ‘GenomicFeatures’ ‘biomaRt’ ‘parallel’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addPseudoAlignment: no visible global function definition for ‘Rle’
annotateRIP: no visible global function definition for ‘getAnnotation’
annotateRIP: no visible global function definition for ‘getBM’
binCount: no visible global function definition for ‘runValue’
binCount: no visible global function definition for ‘seqlengths’
combineRIP: no visible global function definition for ‘seqlengths<-’
combineRIP: no visible global function definition for ‘seqlengths’
computeRPKM: no visible global function definition for ‘exonsBy’
computeRPKM: no visible global function definition for ‘cdsBy’
computeRPKM: no visible global function definition for
‘intronsByTranscript’
computeRPKM: no visible global function definition for
‘fiveUTRsByTranscript’
computeRPKM: no visible global function definition for
‘threeUTRsByTranscript’
computeRPKM: no visible global function definition for ‘seqlevels<-’
computeRPKM: no visible global function definition for ‘seqlevels’
computeRPKM: no visible global function definition for ‘getBM’
galp2gal: no visible global function definition for ‘seqlengths’
getAlignGal: no visible global function definition for ‘seqlengths<-’
getAlignGal: no visible global function definition for ‘seqlengths’
getAlignGal: no visible global function definition for ‘runValue’
getAlignGal: no visible global function definition for ‘Rle’
mainSeek: no visible global function definition for ‘mclapply’
mainSeekSingleChrom: no visible global function definition for
‘runValue’
mainSeekSingleChrom: no visible global function definition for
‘seqlengths’
plotCoverage: no visible global function definition for ‘runValue’
plotCoverage: no visible global function definition for ‘seqlengths’
rulebaseRIPSeek: no visible global function definition for ‘metadata’
rulebaseRIPSeek: no visible global function definition for ‘getBM’
seekRIP: no visible global function definition for ‘runValue’
selectBinSize: no visible global function definition for ‘seqlengths’
viewRIP: no visible global function definition for ‘runValue’
viewRIP: no visible global function definition for
‘GRangesForUCSCGenome’
Undefined global functions or variables:
GRangesForUCSCGenome Rle cdsBy exonsBy fiveUTRsByTranscript
getAnnotation getBM intronsByTranscript mclapply metadata runValue
seqlengths seqlengths<- seqlevels seqlevels<- threeUTRsByTranscript
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
‘SD.aux’, ‘nar.aux’
Please remove them from your package.
* checking examples ... ERROR
Running examples in ‘RIPSeeker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: galp2gal
> ### Title: Convert GAlignmentPairs to GAlignments
> ### Aliases: galp2gal
>
> ### ** Examples
>
> library(Rsamtools)
>
> extdata.dir <- system.file("extdata", package="RIPSeeker")
>
> ex1_file <- list.files(extdata.dir, "ex1.bam", recursive=TRUE, full.names=TRUE)
>
> galp <- readGAlignmentPairs(ex1_file, use.names=TRUE)
>
> galp
GAlignmentPairs object with 1572 pairs, strandMode=1, and 0 metadata columns:
seqnames strand : ranges -- ranges
<Rle> <Rle> : <IRanges> -- <IRanges>
EAS54_61:4:143:69:578 seq1 + : [36, 70] -- [185, 219]
B7_593:4:106:316:452 seq1 + : [49, 84] -- [224, 259]
EAS54_65:3:321:311:983 seq1 + : [51, 85] -- [228, 262]
B7_591:5:42:540:501 seq1 + : [60, 95] -- [224, 259]
EAS192_3:5:223:142:410 seq1 + : [60, 94] -- [235, 269]
... ... ... ... ... ... ...
EAS139_11:5:52:1278:1478 seq2 - : [1513, 1547] -- [1322, 1356]
EAS1_97:4:274:287:423 seq2 - : [1515, 1549] -- [1332, 1366]
EAS54_71:8:105:854:975 seq2 - : [1523, 1555] -- [1354, 1388]
EAS139_11:7:50:1229:1313 seq2 - : [1528, 1562] -- [1376, 1410]
EAS114_26:7:37:79:581 seq2 - : [1533, 1567] -- [1349, 1383]
-------
seqinfo: 2 sequences from an unspecified genome
>
> gal <- galp2gal(galp)
Error in start(right(galp)) :
error in evaluating the argument 'x' in selecting a method for function 'start': Error: The left() and right() getters are defunct for GAlignmentPairs objects.
Calls: galp2gal ... paste -> standardGeneric -> eval -> eval -> eval -> start
Execution halted
* 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.