GUIDEseq 1.5.4
Lihua Julie Zhu
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GUIDEseq | | Last Changed Rev: 126572 / Revision: 127142 | | Last Changed Date: 2017-02-07 16:03:10 -0500 (Tue, 07 Feb 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GUIDEseq_1.5.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GUIDEseq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GUIDEseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GUIDEseq’ version ‘1.5.4’
* 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 ‘GUIDEseq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
extdata 10.5Mb
* 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 ... NOTE
annotateOffTargets: no visible binding for global variable
'offTarget_Start'
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
'seqlevelsStyle<-'
annotateOffTargets: no visible global function definition for 'genes'
annotateOffTargets: no visible global function definition for 'toTable'
getPeaks: no visible binding for global variable 'adjusted.p.value'
getPeaks: no visible binding for global variable 'SNratio'
getUniqueCleavageEvents: no visible binding for global variable
'qwidth.first'
getUniqueCleavageEvents: no visible binding for global variable
'qwidth.last'
getUniqueCleavageEvents: no visible binding for global variable
'strand.last'
getUniqueCleavageEvents: no visible binding for global variable
'strand.first'
getUniqueCleavageEvents: no visible binding for global variable
'readName'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
'gRNAPlusPAM'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
'offTarget'
Undefined global functions or variables:
SNratio adjusted.p.value exons gRNAPlusPAM genes offTarget
offTarget_Start qwidth.first qwidth.last readName seqlevelsStyle<-
strand.first strand.last toTable
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:33-35: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:43-45: Dropping empty section \references
prepare_Rd: createBarcodeFasta.Rd:42-43: Dropping empty section \value
prepare_Rd: createBarcodeFasta.Rd:44-46: Dropping empty section \references
prepare_Rd: getUsedBarcodes.Rd:39-41: Dropping empty section \references
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GUIDEseq-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: createBarcodeFasta
> ### Title: Create barcode as fasta file format for building bowtie1 index
> ### Aliases: createBarcodeFasta
> ### Keywords: manip utilities
>
> ### ** Examples
>
> p7 <- system.file("extdata", "p7.index",
+ package = "GUIDEseq")
> p5 <- system.file("extdata", "p5.index",
+ package = "GUIDEseq")
> outputFile <- "barcodes.fa"
> createBarcodeFasta(p5.index = p5, p7.index = p7, reverse.p7 = TRUE,
+ reverse.p5 = FALSE, outputFile = outputFile)
Warning in file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former
Error in read.table(p7.index, header = header, stringsAsFactors = FALSE) :
no lines available in input
Calls: createBarcodeFasta -> read.table
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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/GUIDEseq.Rcheck/00check.log’
for details.