Package: motifRG

Version: 1.24.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:motifRG.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings motifRG_1.24.0.tar.gz

StartedAt: 2018-10-16 02:08:54 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 02:12:34 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 219.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: motifRG.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:motifRG.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings motifRG_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/motifRG.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifRG/DESCRIPTION’ ... OK
* this is package ‘motifRG’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biostrings’ ‘IRanges’ ‘seqLogo’ ‘parallel’ ‘grid’ ‘BSgenome’
  ‘XVector’ ‘BSgenome.Hsapiens.UCSC.hg19’
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 ‘motifRG’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’ ‘IRanges’ ‘seqLogo’ ‘parallel’ ‘methods’ ‘grid’ ‘graphics’ ‘XVector’
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 ... NOTE
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BSgenome.Hsapiens.UCSC.hg19’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bestPWMMatch: no visible global function definition for ‘Rle’
discretize.glm: no visible global function definition for ‘glm.fit’
findMotif : refinePattern: no visible global function definition for
  ‘t.test’
findMotif : refinePattern: no visible global function definition for
  ‘new’
findPatternView: no visible global function definition for ‘as’
getScore: no visible global function definition for ‘binomial’
getScore : <anonymous>: no visible global function definition for
  ‘glm.fit’
getScore : <anonymous>: no visible global function definition for
  ‘summary.glm’
matchPWMCoor: no visible global function definition for ‘as’
matchPWMCoor: no visible global function definition for ‘GRanges’
motifHtmlTable: no visible global function definition for ‘png’
motifHtmlTable: no visible global function definition for ‘par’
motifHtmlTable: no visible global function definition for ‘dev.off’
motifLatexTable: no visible global function definition for ‘pdf’
motifLatexTable: no visible global function definition for ‘par’
motifLatexTable: no visible global function definition for ‘dev.off’
plotPWM: no visible global function definition for ‘axis’
plotPWM: no visible global function definition for ‘par’
plotPWM: no visible global function definition for ‘col2rgb’
plotPWM: no visible global function definition for ‘rgb’
plotPWM: no visible global function definition for ‘points’
plotPair: no visible global function definition for ‘rgb’
plotPair: no visible global function definition for ‘lines’
Undefined global functions or variables:
  GRanges Rle as axis binomial col2rgb dev.off glm.fit lines new par
  pdf png points rgb summary.glm t.test
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "png", "rgb")
  importFrom("graphics", "axis", "lines", "par", "points")
  importFrom("methods", "as", "new")
  importFrom("stats", "binomial", "glm.fit", "summary.glm", "t.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: YY1.control.Rd:8-9: Dropping empty section \details
prepare_Rd: YY1.peak.Rd:8-9: Dropping empty section \details
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘motifRG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findMotif
> ### Title: De-novo discovery of distriminative motifs
> ### Aliases: findMotif
> 
> ### ** Examples
> 
> MD.peak.seq <- readDNAStringSet(system.file("extdata","MD.peak.fa", package="motifRG"))
> MD.control.seq <- readDNAStringSet(system.file("extdata","MD.control.fa", package="motifRG"))
> category <- c(rep(1, length(MD.peak.seq)), rep(0, length(MD.control.seq)))
> MD.motifs <- findMotif(append(MD.peak.seq, MD.control.seq),category, max.motif=3,enriched=TRUE)
ACAGCT 4.040944e-08 
 Refine  ACAGCT 15.98224 : 15.85959 15.96115 15.70311 16.12329 15.2836 TRUE 771 155 519 138 
ACAGCTV 16.32628 : 16.50829 17.53229 16.25278 16.07341 16.34703 719 109 
NCAGCTV 21.6892 : 21.92678 21.95465 21.73554 20.68249 21.74645 2148 439 
NCAGCTG 22.14095 : 23.30983 22.13691 22.40094 22.44052 22.15941 1787 142 
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
NCASCTG 23.83386 : 23.33209 23.13714 23.8211 23.94959 24.2929 2204 317 
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
New motif:  CASCTG 
match range  1544 
[1] "Rescore"
[1] "Finished Rescore"
CAGCAG 1.649573e-05 
 Refine  CAGCAG 9.144778 : 9.958949 9.511258 9.027596 8.179538 8.089447 TRUE 457 166 328 144 
CAGCVG 10.8216 : 10.74497 11.70443 10.87547 10.90073 11.28597 628 212 
New motif:  CAGCVG 
match range  767 
[1] "Rescore"
[1] "Finished Rescore"
CAGATG 4.196727e-05 
Skip pattern  TTAAAA AAAAGA AAAAAT ATAAAA AAAATA TAAAAA AAAATT AAAAAG AAATAA ATTAAA ATTTTA AGAAAA TTTAAA 
 Refine  CAGATG 7.732073 : 7.14636 7.657593 6.648961 8.629508 8.67028 TRUE 331 149 283 137 
CAGHTG 8.831309 : 9.037463 9.034604 9.318242 9.874017 7.424591 553 279 
New motif:  CAGHTG 
> 
> ### Get summary of motifs
> summaryMotif(MD.motifs$motifs, MD.motifs$category)
Warning: non-unique value when setting 'row.names': ‘NNCAGCTGNN’
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
Calls: summaryMotif ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
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, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/motifRG.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL motifRG
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘motifRG’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifRG)

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