Package: LowMACA

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.10.0.tar.gz

StartedAt: 2018-04-05 05:43:14 -0400 (Thu, 05 Apr 2018)

EndedAt: 2018-04-05 05:47:01 -0400 (Thu, 05 Apr 2018)

EllapsedTime: 227.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: LowMACA.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/LowMACA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LowMACA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LowMACA’ version ‘1.10.0’
* 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 ‘LowMACA’ 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 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 ... OK
* 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 ‘LowMACA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LowMACA-class
> ### Title: Class '"LowMACA"'
> ### Aliases: LowMACA-class alignSequences,LowMACA-method
> ###   bpAll,LowMACA-method entropy,LowMACA-method
> ###   getMutations,LowMACA-method lfm,LowMACA-method lmPlot,LowMACA-method
> ###   mapMutations,LowMACA-method nullProfile,LowMACA-method
> ###   parallelize,LowMACA-method parallelize<-,LowMACA-method
> ###   lmAlignment,LowMACA-method lmMutations,LowMACA-method
> ###   lmEntropy,LowMACA-method lmParams,LowMACA-method
> ###   lmParams<-,LowMACA-method protter,LowMACA-method setup,LowMACA-method
> ###   show,LowMACA-method lfmSingleSequence,LowMACA-method
> ###   lmPlotSingleSequence,LowMACA-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> #ANALYSIS OF SOME OF THE PROTEINS THAT SHARE THE HOMEOBOX DOMAIN
> #Genes to analyze
> Genes <- c("ADNP","ALX1","ALX4","ARGFX","CDX4","CRX"
+   		,"CUX1","CUX2","DBX2","DLX5","DMBX1","DRGX"
+ 			,"DUXA","ESX1","EVX2","HDX","HLX","HNF1A"
+ 			,"HOXA1","HOXA2","HOXA3","HOXA5","HOXB1","HOXB3"
+ 			,"HOXD3","ISL1","ISX","LHX8")
> #Pfam to analyze
> Pfam <- "PF00046"
> #Construct a new LowMACA object
> lm <- newLowMACA(genes=Genes , pfam=Pfam)
All Gene Symbols correct!
> #Change some parameters
> lmParams(lm)[['tumor_type']] <- c("skcm" , "stad" , "ucec" , "luad" , "lusc" , "coadread" , "brca")
> lmParams(lm)[['min_mutation_number']] <- 1
> lmParams(lm)[['density_bw']] <- 0
> #Run if you have clustalo installed
> lm <- setup(lm)
Aligning sequences...
Getting mutations from cancers studies...
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 6 elements
Calls: setup ... processURL -> processURL.CGDS -> read.table -> scan
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
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/LowMACA.Rcheck/00check.log’
for details.

* installing *source* package ‘LowMACA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* DONE (LowMACA)

name	user	system	elapsed
BLOSUM62	0.011	0.002	0.013