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BioC 3.6: CHECK report for annmap on veracruz1

This page was generated on 2017-08-16 13:42:57 -0400 (Wed, 16 Aug 2017).

Package 46/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annmap 1.19.0
Chris Wirth
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annmap
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: annmap
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annmap_1.19.0.tar.gz
StartedAt: 2017-08-15 23:52:20 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:57:51 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 330.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: annmap.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annmap_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/annmap.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘annmap’ version ‘1.19.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annmap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
'library' or 'require' call to ‘rjson’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.make.hash’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.coerce: no visible global function definition for ‘setNames’
.coerce: no visible binding for global variable ‘v’
.coerce: no visible binding for global variable ‘k’
.get.stats.cache: no visible global function definition for
  ‘flush.console’
.layout.genes: no visible global function definition for ‘strwidth’
.load.and.parse: no visible global function definition for ‘fromJSON’
.read.databases: no visible global function definition for ‘read.table’
.single.transcript.coords.to.genome: no visible global function
  definition for ‘tail’
.xmc.connect: no visible global function definition for ‘menu’
.xmcws.connect: no visible global function definition for ‘fromJSON’
.xmcws.connect: no visible global function definition for ‘menu’
annmapAddConnection: no visible global function definition for
  ‘write.table’
annmapConnect: no visible global function definition for
  ‘install.packages’
arrayType: no visible global function definition for ‘menu’
convertBamToRle : <anonymous>: no visible global function definition
  for ‘Rle’
geneToGeneRegionTrack : generate: no visible global function definition
  for ‘GeneRegionTrack’
generateBridgeData: no visible global function definition for ‘rainbow’
genomicPlot : <anonymous>: no visible global function definition for
  ‘rgb’
genomicPlot: no visible global function definition for ‘rgb’
ngsTracePlotter : local.draw: no visible global function definition for
  ‘runValue’
ngsTracePlotter: no visible global function definition for ‘modifyList’
ngsTraceScale : <anonymous>: no visible global function definition for
  ‘runValue’
seqnameMapping: no visible global function definition for ‘seqlevels<-’
seqnameMapping: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  GeneRegionTrack Rle flush.console fromJSON install.packages k menu
  modifyList rainbow read.table rgb runValue seqlevels seqlevels<-
  setNames strwidth tail v write.table
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "strwidth")
  importFrom("stats", "setNames")
  importFrom("utils", "flush.console", "install.packages", "menu",
             "modifyList", "read.table", "tail", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plot.ngs.Rd':
  ‘[IRanges]{Rle}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* 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 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/annmap.Rcheck/00check.log’
for details.


annmap.Rcheck/00install.out:

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

annmap.Rcheck/annmap-Ex.timings:

nameusersystemelapsed
annmap.all000
annmap.coords0.0060.0000.007
annmap.details0.0010.0000.006
annmap.env0.0020.0000.002
annmap.filters0.0010.0010.002
annmap.range0.0030.0000.008
annmap.seqname0.0010.0010.001
annmap.spliceIndex0.0010.0000.001
annmap.to0.0010.0000.001
annmap.utils0.0010.0000.001
annmap.utr0.0010.0000.000