R Development Page

patchwork log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2017-02-03-13-43/RF_PKG_CHECK/PKGS/patchwork.Rcheck'
* using R version 3.3.2 Patched (2017-01-31 r72064)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'patchwork/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'patchwork' version '2.4'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Markus Mayrhofer '

New submission

Unknown, possibly mis-spelled, fields in DESCRIPTION:
  '#Imports'

The Title field should be in title case, current version then in title case:
'Allele-specific Copy Number Analysis of whole genome data'
'Allele-Specific Copy Number Analysis of Whole Genome Data'

The Date field is not in ISO 8601 yyyy-mm-dd format.
* 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 whether package 'patchwork' can be installed ... OK
* checking installed package size ... OK
* checking package 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'DNAcopy' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'patchwork/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage("Welcome to patchwork.")
    packageStartupMessage("\n")
    packageStartupMessage("Version: ", utils::packageDescription("patchwork")$Version)
    packageStartupMessage("\n")
    packageStartupMessage("If this is your first time running patchwork you should visit the")
    packageStartupMessage("homepage at (http://patchwork.r-forge.r-project.org/) or see ?patchwork.readme")
    packageStartupMessage("or the README file found at the install location of patchwork/inst/README")
    packageStartupMessage("\n")
    packageStartupMessage("Remember to keep patchwork up to date: update.packages(repos=\"http://R-Forge.R-project.org\")")

See section 'Good practice' in '?.onAttach'.

karyotype: no visible global function definition for 'colorRampPalette'
karyotype: no visible global function definition for 'jpeg'
karyotype: no visible global function definition for 'split.screen'
karyotype: no visible global function definition for 'screen'
karyotype: no visible global function definition for 'par'
karyotype: no visible global function definition for 'plot'
karyotype: no visible global function definition for 'segments'
karyotype: no visible global function definition for 'box'
karyotype: no visible global function definition for 'mtext'
karyotype: no visible global function definition for 'axis'
karyotype: no visible global function definition for 'rect'
karyotype: no visible global function definition for 'close.screen'
karyotype: no visible global function definition for 'dev.off'
karyotype_check: no visible global function definition for 'png'
karyotype_check: no visible global function definition for 'plot'
karyotype_check: no visible global function definition for 'axis'
karyotype_check: no visible global function definition for 'title'
karyotype_check: no visible global function definition for 'text'
karyotype_check: no visible global function definition for 'dev.off'
karyotype_chroms: no visible global function definition for
  'colorRampPalette'
karyotype_chroms: no visible global function definition for 'jpeg'
karyotype_chroms: no visible global function definition for
  'split.screen'
karyotype_chroms: no visible global function definition for 'screen'
karyotype_chroms: no visible global function definition for 'par'
karyotype_chroms: no visible global function definition for 'plot'
karyotype_chroms: no visible global function definition for 'points'
karyotype_chroms: no visible global function definition for 'axis'
karyotype_chroms: no visible global function definition for 'mtext'
karyotype_chroms: no visible global function definition for 'segments'
karyotype_chroms: no visible global function definition for 'rect'
karyotype_chroms: no visible global function definition for 'text'
karyotype_chroms: no visible global function definition for
  'close.screen'
karyotype_chroms: no visible global function definition for 'dev.off'
karyotype_chromsCN: no visible global function definition for
  'colorRampPalette'
karyotype_chromsCN: no visible global function definition for 'jpeg'
karyotype_chromsCN: no visible global function definition for
  'split.screen'
karyotype_chromsCN: no visible global function definition for 'screen'
karyotype_chromsCN: no visible global function definition for 'par'
karyotype_chromsCN: no visible global function definition for 'plot'
karyotype_chromsCN: no visible global function definition for 'points'
karyotype_chromsCN: no visible global function definition for 'axis'
karyotype_chromsCN: no visible global function definition for 'text'
karyotype_chromsCN: no visible global function definition for 'mtext'
karyotype_chromsCN: no visible global function definition for
  'segments'
karyotype_chromsCN: no visible global function definition for 'rect'
karyotype_chromsCN: no visible global function definition for
  'close.screen'
karyotype_chromsCN: no visible global function definition for 'dev.off'
patchwork.GCNorm: no visible global function definition for 'median'
patchwork.GCNorm: no visible global function definition for 'sd'
patchwork.Medians_n_AI: no visible global function definition for
  'median'
patchwork.alleledata: no visible global function definition for
  'read.csv'
patchwork.alleledata: no visible global function definition for 'data'
patchwork.alleledata: no visible binding for global variable
  'commonSnpsHG18'
patchwork.alleledata: no visible binding for global variable
  'commonSnps132'
patchwork.copynumbers: no visible binding for global variable 'segs'
patchwork.copynumbers: no visible global function definition for
  'write.csv'
patchwork.copynumbers: no visible binding for global variable 'kbsegs'
patchwork.copynumbers: no visible binding for global variable 'alf'
patchwork.readChroms: no visible global function definition for
  'read.csv'
patchwork.readChroms: no visible global function definition for 'hist'
patchwork.region: no visible binding for global variable 'segs'
patchwork.region: no visible binding for global variable 'kbsegs'
patchwork.region: no visible binding for global variable 'alf'
patchwork.region: no visible global function definition for
  'colorRampPalette'
patchwork.region: no visible global function definition for 'jpeg'
patchwork.region: no visible global function definition for
  'split.screen'
patchwork.region: no visible global function definition for 'screen'
patchwork.region: no visible global function definition for 'par'
patchwork.region: no visible global function definition for 'plot'
patchwork.region: no visible global function definition for 'axis'
patchwork.region: no visible global function definition for 'mtext'
patchwork.region: no visible global function definition for 'segments'
patchwork.region: no visible global function definition for 'rect'
patchwork.region: no visible global function definition for 'text'
patchwork.region: no visible global function definition for 'rgb'
patchwork.region: no visible global function definition for
  'close.screen'
patchwork.region: no visible global function definition for 'dev.off'
patchwork.segment: no visible global function definition for 'data'
patchwork.segment: no visible global function definition for 'segment'
patchwork.segment: no visible global function definition for
  'smooth.CNA'
patchwork.segment: no visible global function definition for 'CNA'
patchwork.smoothing: no visible global function definition for 'median'
weightedMedian: no visible global function definition for 'median'
Undefined global functions or variables:
  CNA alf axis box close.screen colorRampPalette commonSnps132
  commonSnpsHG18 data dev.off hist jpeg kbsegs median mtext par plot
  png points read.csv rect rgb screen sd segment segments segs
  smooth.CNA split.screen text title write.csv
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "jpeg", "png",
             "rgb")
  importFrom("graphics", "axis", "box", "close.screen", "hist", "mtext",
             "par", "plot", "points", "rect", "screen", "segments",
             "split.screen", "text", "title")
  importFrom("stats", "median", "sd")
  importFrom("utils", "data", "read.csv", "write.csv")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File 'patchwork/R/patchwork.alleledata.r':
  data(commonSnpsHG18, package = "patchworkData")
  data(commonSnps132, package = "patchworkData")
File 'patchwork/R/patchwork.copynumbers.r':
  data(ideogram, package = "patchworkData")
File 'patchwork/R/patchwork.createreference.r':
  data(ideogram, package = "patchworkData")
File 'patchwork/R/patchwork.plot.r':
  data(ideogram, package = "patchworkData")
File 'patchwork/R/patchwork.segment.r':
  data(ideogram, package = "patchworkData")
File 'patchwork/R/patchwork.smoothing.r':
  data(ideogram, package = "patchworkData")
See section 'Good practice' in '?data'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'karyotype.Rd':
  \usage lines wider than 90 characters:
     karyotype(chr,start,end,int,ai,mchr,mpos,mval,schr,spos,sval,name='',xlim=c(0,2.5),ylim=c(0,1),MAPD=" ",MHOF=" ")

Rd file 'karyotype_chroms.Rd':
  \usage lines wider than 90 characters:
     karyotype_chroms(chr,start,end,int,ai,mchr,mpos,mval,schr,spos,sval,name='',xlim=c(0,2.5),ylim=0:1,MAPD=" ",MHOF=" ")

Rd file 'karyotype_chromsCN.Rd':
  \usage lines wider than 90 characters:
     karyotype_chromsCN(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,schr,spos,sval,t,name='',parameters,xlim=c(0,2.5),ylim=0:1,maxCn=8)

Rd file 'patchwork.copynumbers.Rd':
  \usage lines wider than 90 characters:
     patchwork.copynumbers(CNfile,cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F,male.sample=F,male2femref=F)

Rd file 'patchwork.plot.Rd':
  \usage lines wider than 90 characters:
     patchwork.plot(Tumor.bam,Tumor.pileup,Tumor.vcf=NULL,Normal.bam=NULL,Normal.pileup=NULL,Normal.vcf=NULL,Reference=NULL,Alpha=0.0001,SD= ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 R/sysdata.rda ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* checking for code which exercises the package ... WARNING
No examples, no tests, no vignettes
* DONE

Status: 1 WARNING, 4 NOTEs
See
  'R:/run/building/build_2017-02-03-13-43/RF_PKG_CHECK/PKGS/patchwork.Rcheck/00check.log'
for details.


Run time: 33.45 seconds.