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BioC 3.4: CHECK report for segmentSeq on morelia

This page was generated on 2017-04-15 16:23:11 -0400 (Sat, 15 Apr 2017).

Package 1119/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.8.0
Thomas J. Hardcastle
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/segmentSeq
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: segmentSeq
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.8.0.tar.gz
StartedAt: 2017-04-15 07:53:31 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 07:58:45 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 313.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: segmentSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/segmentSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.8.0’
* 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 ‘segmentSeq’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... 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
.classifyNulls: no visible global function definition for ‘runif’
.constructNullPriors: no visible global function definition for ‘runif’
.constructNulls: no visible global function definition for ‘runif’
.getLocLikelihoods : NBdens : PDgivenr.NB: no visible global function
  definition for ‘dnbinom’
.getLocLikelihoods : BBdens : PDgivenr.BB : dbetabinom: no visible
  global function definition for ‘dbinom’
.massiveClassifyLoci: no visible global function definition for ‘runif’
.methFunction: no visible global function definition for ‘pbeta’
.plotSampleMeth: no visible global function definition for ‘lines’
.processPosts: no visible global function definition for ‘runif’
.subProfile : <anonymous> : summariseCoverage : <anonymous>: no visible
  global function definition for ‘weighted.mean’
plotAverageProfile: no visible global function definition for ‘rainbow’
plotAverageProfile : <anonymous>: no visible global function definition
  for ‘lines’
plotAverageProfile: no visible global function definition for ‘abline’
plotAverageProfile: no visible global function definition for ‘dev.cur’
plotAverageProfile: no visible global function definition for ‘par’
plotAverageProfile : <anonymous>: no visible global function definition
  for ‘rainbow’
plotAverageProfile: no visible global function definition for ‘title’
plotAverageProfile: no visible global function definition for ‘lines’
plotAverageProfile: no visible global function definition for
  ‘weighted.mean’
plotMeth: no visible global function definition for ‘par’
plotMeth : <anonymous>: no visible global function definition for
  ‘abline’
plotMethDistribution: no visible global function definition for
  ‘rainbow’
readBAM : <anonymous>: no visible global function definition for
  ‘write.table’
readGeneric : <anonymous>: no visible global function definition for
  ‘read.table’
readGeneric : <anonymous>: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline dbinom dev.cur dnbinom lines par pbeta rainbow read.table
  runif title weighted.mean write.table
Consider adding
  importFrom("grDevices", "dev.cur", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "title")
  importFrom("stats", "dbinom", "dnbinom", "pbeta", "runif",
             "weighted.mean")
  importFrom("utils", "read.table", "write.table")
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:
  ‘normaliseNC’
Undocumented S4 methods:
  generic '[' and siglist 'alignmentClass,ANY,ANY,ANY'
  generic '[' and siglist 'alignmentData,ANY,ANY,ANY'
  generic '[' and siglist 'alignmentMeth,ANY,ANY,ANY'
  generic '[' and siglist 'lociData,ANY,ANY,ANY'
  generic '[' and siglist 'methData,ANY,ANY,ANY'
  generic '[' and siglist 'segClass,ANY,ANY,ANY'
  generic '[' and siglist 'segData,ANY,ANY,ANY'
  generic '[' and siglist 'segMeth,ANY,ANY,ANY'
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 sizes of PDF files under ‘inst/doc’ ... 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
classifySeg     34.199  0.245  34.515
lociLikelihoods 13.792  0.069  13.886
heuristicSeg    12.103  0.040  12.151
readMeths        8.870  0.457   9.332
plotGenome       6.249  0.035   6.292
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.


segmentSeq.Rcheck/00install.out:

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

segmentSeq.Rcheck/segmentSeq-Ex.timings:

nameusersystemelapsed
alignmentData-class2.1380.0222.162
classifySeg34.199 0.24534.515
findChunks2.3000.0142.315
getCounts3.5330.0143.552
getOverlaps2.4040.0132.419
heuristicSeg12.103 0.04012.151
lociLikelihoods13.792 0.06913.886
plotGenome6.2490.0356.292
processAD3.2280.0103.240
readMethods2.4680.0102.481
readMeths8.8700.4579.332
segData-class2.8410.0202.863
segmentSeq-package2.9650.0132.981