GUIDEseq 1.3.14
Lihua Julie Zhu
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GUIDEseq | | Last Changed Rev: 120996 / Revision: 121152 | | Last Changed Date: 2016-09-16 04:32:55 -0700 (Fri, 16 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | ERROR | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GUIDEseq_1.3.14.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GUIDEseq.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 ‘GUIDEseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GUIDEseq’ version ‘1.3.14’
* 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 11.1Mb
sub-directories of 1Mb or more:
extdata 10.6Mb
* 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 loading without being on the library search path ... 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 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
qwidth.first qwidth.last readName seqlevelsStyle<- strand.first
strand.last toTable
* 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 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: combineOfftargets
> ### Title: Combine Offtargets
> ### Aliases: combineOfftargets
> ### Keywords: misc
>
> ### ** Examples
>
> offtarget.folder <- system.file("extdata",
+ c("sample1-17", "sample2-18", "sample3-19"),
+ package = "GUIDEseq")
> mergedOfftargets <-
+ combineOfftargets(offtarget.folder = offtarget.folder,
+ sample.name = c("cas9Only", "WT SpCas9", "SpCas9-MT3-ZFP"),
+ outputFileName = "TS2offtargets3Constructs.xls")
Error in `[.data.frame`(all, , i) : undefined columns selected
Calls: combineOfftargets ... do.call -> lapply -> lapply -> FUN -> [ -> [.data.frame
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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/GUIDEseq.Rcheck/00check.log’
for details.