BioC experimental data: CHECK report for yriMulti on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings yriMulti_0.0.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/yriMulti.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70434)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yriMulti/DESCRIPTION’ ... OK
* this is package ‘yriMulti’ version ‘0.0.9’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘gQTLBase’ ‘SummarizedExperiment’ ‘GenomicRanges’ ‘Homo.sapiens’
  ‘dsQTL’ ‘geuvPack’
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 ‘yriMulti’ can be installed ... [31s/32s] OK
* checking installed package size ... NOTE
  installed size is 172.6Mb
  sub-directories of 1Mb or more:
    data  172.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘Homo.sapiens’ ‘SummarizedExperiment’ ‘dsQTL’
  ‘gQTLBase’ ‘geuvPack’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindelms : <anonymous>: no visible global function definition for ‘lm’
bindelms: no visible global function definition for ‘mcols’
bindelms: no visible global function definition for ‘mcols<-’
bindelms: no visible global function definition for ‘metadata<-’
checkGenomes: no visible global function definition for ‘genome’
mexDF: no visible global function definition for ‘mcols’
mexGR: no visible global function definition for ‘mcols’
mexGR: no visible global function definition for ‘findOverlaps’
mexGR: no visible global function definition for ‘rowRanges’
mexGR: no visible global function definition for ‘subjectHits’
mexGR : embell: no visible global function definition for ‘DataFrame’
mexGR : embell: no visible global function definition for ‘assays’
mexGR : embell: no visible global function definition for ‘start’
mexGR : embell: no visible global function definition for ‘end’
mexGR : embell: no visible global function definition for ‘strand’
mexGR : embell: no visible global function definition for ‘seqnames’
mexGR: no visible global function definition for ‘GRanges’
mexGR: no visible global function definition for ‘IRanges’
mexGR: no visible global function definition for ‘mcols<-’
mexGR: no visible global function definition for ‘seqinfo<-’
mexGR: no visible global function definition for ‘seqinfo’
plotEvM: no visible global function definition for ‘mcols’
plotEvM: no visible global function definition for ‘metadata’
plotEvM: no visible global function definition for ‘plot’
plotEvM: no visible global function definition for ‘abline’
plotEvM: no visible global function definition for ‘coef’
symind: no visible global function definition for ‘mcols’
show,mexGR: no visible global function definition for ‘mcols’
show,mexGR: no visible global function definition for ‘selectSome’
Undefined global functions or variables:
  DataFrame GRanges IRanges abline assays coef end findOverlaps genome
  lm mcols mcols<- metadata metadata<- plot rowRanges selectSome
  seqinfo seqinfo<- seqnames start strand subjectHits
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "end", "lm", "start")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: mexGR.Rd:32-34: Dropping empty section \details
prepare_Rd: mexGR.Rd:49-51: Dropping empty section \note
prepare_Rd: mexGR.Rd:46-48: Dropping empty section \author
prepare_Rd: mexGR.Rd:43-45: Dropping empty section \references
prepare_Rd: mexGR.Rd:55-57: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘bindelms’ ‘checkGenomes’ ‘mexDF’ ‘plotEvM’ ‘symind’
Undocumented data sets:
  ‘banovichSE’
Undocumented S4 classes:
  ‘mexGR’
Undocumented S4 methods:
  generic 'show' and siglist 'mexGR'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  banovichSE.rda  172.2Mb  114.9Mb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
mexGR 14.278  0.164  14.497
* 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: 2 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-data-experiment/meat/yriMulti.Rcheck/00check.log’
for details.
BioC experimental data: CHECK report for yriMulti on zin2

Summary

Command output
