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BioC 3.6: CHECK report for erma on malbec1

This page was generated on 2017-08-16 13:23:24 -0400 (Wed, 16 Aug 2017).

Package 420/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erma 0.9.2
VJ Carey
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/erma
Last Changed Rev: 130713 / Revision: 131943
Last Changed Date: 2017-06-27 13:05:27 -0400 (Tue, 27 Jun 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: erma
Version: 0.9.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings erma_0.9.2.tar.gz
StartedAt: 2017-08-15 22:59:04 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:03:29 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 264.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: erma.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings erma_0.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/erma.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘erma/DESCRIPTION’ ... OK
* this is package ‘erma’ version ‘0.9.2’
* 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 ‘erma’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 199.7Mb
  sub-directories of 1Mb or more:
    bed_tabix  161.3Mb
    data        37.1Mb
* 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 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
geneTxRange: no visible global function definition for ‘select’
geneTxRange: no visible global function definition for ‘IRanges’
genemodel: no visible global function definition for ‘IRanges’
genemodelOLD: no visible binding for global variable ‘exonsBy’
map2range: no visible global function definition for ‘IRanges’
mapmeta: no visible global function definition for ‘read.csv’
stateProf: no visible global function definition for ‘keys’
stateProfile: no visible binding for global variable ‘i’
stateProfile: no visible global function definition for ‘genome’
stateProfile: no visible global function definition for ‘seqlevels<-’
stateProfile: no visible global function definition for ‘seqlevels’
stateProfile : <anonymous>: no visible global function definition for
  ‘IRanges’
stateProfile: no visible global function definition for ‘data’
stateProfile: no visible binding for global variable ‘short_celltype’
stateProfile: no visible binding for global variable ‘states_25’
stateProfile: no visible binding for global variable ‘name’
statesByRange: no visible binding for global variable ‘mod’
statesByRange: no visible binding for global variable ‘upstream’
statesByRange: no visible binding for global variable ‘downstream’
statesByRange: no visible binding for global variable ‘i’
statesByRange: no visible global function definition for ‘genome’
statesByRange: no visible global function definition for ‘seqlevels<-’
statesByRange: no visible global function definition for ‘seqlevels’
statesByRange : <anonymous>: no visible global function definition for
  ‘IRanges’
statesByRange : <anonymous>: no visible binding for global variable
  ‘tss’
statesByRange: no visible global function definition for ‘data’
statesByRange: no visible binding for global variable ‘short_celltype’
statesByRange: no visible binding for global variable ‘states_25’
subsetByRanges : <anonymous>: no visible global function definition for
  ‘genome’
subsetByRanges : <anonymous>: no visible global function definition for
  ‘seqlevels<-’
subsetByRanges : <anonymous>: no visible global function definition for
  ‘seqlevels’
Undefined global functions or variables:
  IRanges data downstream exonsBy genome i keys mod name read.csv
  select seqlevels seqlevels<- short_celltype states_25 tss upstream
Consider adding
  importFrom("utils", "data", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘subsetByRanges’
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 ... WARNING
Codoc mismatches from documentation object 'stateProfile':
stateProf
  Code: function(ermaset, shortCellType = FALSE, ctsize = 10, iniSym =
                 "IL7R")
  Docs: function(ermaset, shortCellType = TRUE, ctsize = 10, iniSym =
                 "IL7R")
  Mismatches in argument default values:
    Name: 'shortCellType' Code: FALSE Docs: TRUE

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'stateProfile'
  ‘iniSym’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
erma-package 8.664  0.364   9.247
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/erma.Rcheck/00check.log’
for details.


erma.Rcheck/00install.out:

* installing *source* package ‘erma’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (erma)

erma.Rcheck/erma-Ex.timings:

nameusersystemelapsed
ErmaSet-class1.0080.0121.021
erma-package8.6640.3649.247
genemodel1.5040.0161.582
mapmeta0.1000.0000.101
stateProfile3.1360.0003.387
states_250.0000.0000.002