Package: yriMulti

Version: 0.8.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings yriMulti_0.8.0.tar.gz

StartedAt: 2018-04-12 10:44:28 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:54:09 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 581.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: yriMulti.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings yriMulti_0.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/yriMulti.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘0.8.0’
* 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 ‘yriMulti’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 179.4Mb
  sub-directories of 1Mb or more:
    data  179.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘geuvPack’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
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
mexGR: no visible global function definition for ‘subjectHits’
mexGR : embell: no visible global function definition for ‘DataFrame’
mexGR: no visible global function definition for ‘IRanges’
mexGR: no visible global function definition for ‘new’
show,mexGR: no visible global function definition for ‘selectSome’
Undefined global functions or variables:
  DataFrame IRanges new selectSome subjectHits
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: pwplot.Rd:7-9: Dropping empty section \description
prepare_Rd: pwplot.Rd:40-42: Dropping empty section \details
checkRd: (5) pwplot.Rd:0-70: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘demoMAE’
All user-level objects in a package 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
  demoMAE.rda       6.8Mb    5.9Mb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mexGR      11.704  0.212  11.949
banovichSE  6.372  0.124   6.498
* 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: 3 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/yriMulti.Rcheck/00check.log’
for details.

* installing *source* package ‘yriMulti’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yriMulti)

name	user	system	elapsed
banovichSE	6.372	0.124	6.498
mexGR	11.704	0.212	11.949
pwplot	0.272	0.000	0.271
yriMulti-package	0	0	0