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BioC 3.4: CHECK report for biomvRCNS on zin1

This page was generated on 2016-09-21 03:38:12 -0700 (Wed, 21 Sep 2016).

Package 120/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomvRCNS 1.13.0
Yang Du
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biomvRCNS
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biomvRCNS
Version: 1.13.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings biomvRCNS_1.13.0.tar.gz
StartedAt: 2016-09-20 03:47:29 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:51:09 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 220.6 seconds
RetCode: 0
Status:  OK 
CheckDir: biomvRCNS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings biomvRCNS_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/biomvRCNS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomvRCNS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomvRCNS’ version ‘1.13.0’
* 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 ‘biomvRCNS’ 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 ... NOTE
'library' or 'require' calls in package code:
  'GenomicFeatures' 'cluster' 'dynamicTreeCut' 'parallel'
  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
biomvRGviz: no visible global function definition for 'rainbow'
biomvRGviz: no visible global function definition for 'hasArg'
biomvRGviz: no visible global function definition for 'graphics.off'
biomvRGviz: no visible global function definition for 'setEPS'
biomvRGviz: no visible global function definition for 'postscript'
biomvRGviz: no visible global function definition for 'pdf'
biomvRGviz: no visible global function definition for 'dev.off'
biomvRhsmm: no visible binding for global variable 'mclapply'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'DataFrame'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'Rle'
biomvRhsmm: no visible global function definition for 'DataFrame'
biomvRhsmm: no visible binding for global variable 'DataFrame'
biomvRhsmm: no visible global function definition for 'new'
biomvRmgmr: no visible global function definition for 'seqlevels<-'
biomvRmgmr: no visible global function definition for 'DataFrame'
biomvRmgmr: no visible global function definition for 'new'
biomvRseg: no visible global function definition for 'seqlevels<-'
biomvRseg: no visible global function definition for 'DataFrame'
biomvRseg: no visible global function definition for 'new'
estEmis: no visible global function definition for 'clara'
gammaFit: no visible global function definition for 'cov.wt'
hsmmRun: no visible global function definition for 'Rle'
hsmmRun : <anonymous>: no visible global function definition for 'Rle'
hsmmRun: no visible global function definition for 'seqlevels<-'
initEmis : <anonymous>: no visible global function definition for
  'dpois'
initEmis : <anonymous>: no visible global function definition for
  'dnorm'
initEmis : <anonymous>: no visible global function definition for
  'dnbinom'
initEmis : <anonymous>: no visible global function definition for
  'cov2cor'
initEmis : <anonymous>: no visible global function definition for 'dt'
initEmis : <anonymous>: no visible global function definition for
  'cov.wt'
initEmis : <anonymous>: no visible global function definition for
  'weighted.mean'
initSojDd : <anonymous>: no visible global function definition for
  'dgamma'
initSojDd : <anonymous>: no visible global function definition for
  'dpois'
initSojDd : <anonymous>: no visible global function definition for
  'dnbinom'
maxGapminRun: no visible global function definition for 'Rle'
maxGapminRun: no visible global function definition for 'runValue'
nbinomCLLDD: no visible global function definition for 'cov.wt'
nbinomCLLDD: no visible global function definition for 'dnbinom'
poisFit : <anonymous>: no visible global function definition for
  'dpois'
preClustGrp: no visible global function definition for 'dist'
preClustGrp: no visible global function definition for 'hclust'
preClustGrp: no visible global function definition for 'cutreeDynamic'
regionSegAlphaNB: no visible global function definition for 'mclapply'
regionSegCost: no visible global function definition for 'mclapply'
simSegData: no visible global function definition for 'runValue'
simSegData: no visible global function definition for 'Rle'
simSegData: no visible global function definition for 'pdf'
simSegData: no visible global function definition for 'ts.plot'
simSegData: no visible global function definition for 'dev.off'
simUvSegData: no visible global function definition for 'rnorm'
simUvSegData: no visible global function definition for 'rt'
simUvSegData: no visible global function definition for 'rgamma'
simUvSegData: no visible global function definition for 'rpois'
simUvSegData: no visible global function definition for 'rnbinom'
sojournAnno: no visible global function definition for 'transcripts'
sojournAnno: no visible global function definition for 'seqlengths'
sojournAnno: no visible global function definition for 'exons'
sojournAnno: no visible global function definition for
  'intronsByTranscript'
splitFarNeighbouryhat: no visible global function definition for
  'runValue'
tmvtfFit: no visible global function definition for 'cov.wt'
unifMJ : <anonymous>: no visible global function definition for 'dunif'
unifMJ : <anonymous> : <anonymous>: no visible global function
  definition for 'dunif'
plot,biomvRCNS-ANY: no visible binding for global variable 'ssetst'
Undefined global functions or variables:
  DataFrame Rle clara cov.wt cov2cor cutreeDynamic dev.off dgamma dist
  dnbinom dnorm dpois dt dunif exons graphics.off hasArg hclust
  intronsByTranscript mclapply new pdf postscript rainbow rgamma
  rnbinom rnorm rpois rt runValue seqlengths seqlevels<- setEPS ssetst
  transcripts ts.plot weighted.mean
Consider adding
  importFrom("grDevices", "dev.off", "graphics.off", "pdf", "postscript",
             "rainbow", "setEPS")
  importFrom("methods", "hasArg", "new")
  importFrom("stats", "cov.wt", "cov2cor", "dgamma", "dist", "dnbinom",
             "dnorm", "dpois", "dt", "dunif", "hclust", "rgamma",
             "rnbinom", "rnorm", "rpois", "rt", "ts.plot",
             "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/biomvRCNS.Rcheck/00check.log’
for details.


biomvRCNS.Rcheck/00install.out:

* installing *source* package ‘biomvRCNS’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c biomvRCNS.c -o biomvRCNS.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o biomvRCNS.so biomvRCNS.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/biomvRCNS.Rcheck/biomvRCNS/libs
** 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 (biomvRCNS)

biomvRCNS.Rcheck/biomvRCNS-Ex.timings:

nameusersystemelapsed
biomvRCNS-class0.0040.0000.001
biomvRGviz1.1400.0081.146
biomvRhsmm3.0280.2683.868
biomvRmgmr0.8720.0240.916
biomvRseg2.1600.0402.209
hsmmRun0.0600.0000.058
maxGapminRun0.0040.0000.004
regionSegAlphaNB0.0920.0000.092
regionSegCost0.0000.0000.001
simSegData0.0040.0000.003
sojournAnno0.0440.0000.043
splitFarNeighbour0.0040.0000.002