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CHECK report for CNVrd2 on merida1

This page was generated on 2019-04-16 11:57:16 -0400 (Tue, 16 Apr 2019).

Package 296/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVrd2 1.20.0
Hoang Tan Nguyen
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/CNVrd2
Branch: RELEASE_3_8
Last Commit: f0332cc
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CNVrd2
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNVrd2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNVrd2_1.20.0.tar.gz
StartedAt: 2019-04-15 23:07:42 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:12:01 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 258.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CNVrd2.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNVrd2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNVrd2_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CNVrd2.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVrd2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVrd2’ version ‘1.20.0’
* 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 ‘CNVrd2’ 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘DNAcopy’ ‘Rsamtools’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘VariantAnnotation’ ‘ggplot2’ ‘gridExtra’ ‘methods’ ‘parallel’
  ‘rjags’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
groupCNVs,clusteringCNVs: warning in matrix(0, nr = length(x2), ncol =
  k - 2): partial argument match of 'nr' to 'nrow'
segmentSamples,CNVrd2: warning in matrix(0, nr = nnn, ncol =
  dim(genes)[2]): partial argument match of 'nr' to 'nrow'
calculateLDSNPandCNV: no visible global function definition for
  ‘TabixFile’
calculateLDSNPandCNV : readChunkVCF: no visible global function
  definition for ‘GRanges’
calculateLDSNPandCNV : readChunkVCF: no visible global function
  definition for ‘readVcf’
calculateLDSNPandCNV : readChunkVCF: no visible global function
  definition for ‘geno’
calculateLDSNPandCNV: no visible global function definition for
  ‘mclapply’
calculateLDSNPandCNV : calcPandR2 : LDandP: no visible global function
  definition for ‘fisher.test’
calculateLDSNPandCNV : calcPandR2 : LDandP: no visible global function
  definition for ‘chisq.test’
calculateLDSNPandCNV : calcPandR2: no visible global function
  definition for ‘p.adjust’
groupBayesianCNVs: no visible global function definition for
  ‘jags.model’
groupBayesianCNVs: no visible global function definition for ‘update’
groupBayesianCNVs: no visible global function definition for
  ‘coda.samples’
groupBayesianCNVs: no visible global function definition for ‘dnorm’
groupBayesianCNVs: no visible global function definition for ‘par’
groupBayesianCNVs: no visible global function definition for ‘plot’
groupBayesianCNVs: no visible global function definition for ‘hist’
countReadInWindow,CNVrd2: no visible global function definition for
  ‘readDNAStringSet’
countReadInWindow,CNVrd2 : countReadForBamFile: no visible global
  function definition for ‘write.table’
countReadInWindow,CNVrd2: no visible binding for global variable
  ‘objectCNVrd2’
countReadInWindow,CNVrd2: no visible global function definition for
  ‘ScanBamParam’
countReadInWindow,CNVrd2 : <anonymous>: no visible global function
  definition for ‘countBam’
countReadInWindow,CNVrd2 : gcContent: no visible global function
  definition for ‘unmasked’
countReadInWindow,CNVrd2 : gcContent: no visible binding for global
  variable ‘Hsapiens’
countReadInWindow,CNVrd2 : gcContent: no visible global function
  definition for ‘alphabetFrequency’
emnormalCNV,clusteringCNVs : loglk : <anonymous>: no visible global
  function definition for ‘dnorm’
emnormalCNV,clusteringCNVs : initialValues: no visible global function
  definition for ‘kmeans’
emnormalCNV,clusteringCNVs: no visible global function definition for
  ‘dnorm’
emnormalCNV,clusteringCNVs : <anonymous>: no visible global function
  definition for ‘dnorm’
groupCNVs,clusteringCNVs: no visible global function definition for
  ‘par’
groupCNVs,clusteringCNVs: no visible global function definition for
  ‘plot’
groupCNVs,clusteringCNVs: no visible global function definition for
  ‘axis’
groupCNVs,clusteringCNVs: no visible global function definition for
  ‘abline’
groupCNVs,clusteringCNVs: no visible global function definition for
  ‘text’
groupCNVs,clusteringCNVs: no visible global function definition for
  ‘hist’
plotCNVrd2,CNVrd2: no visible global function definition for ‘plot’
plotCNVrd2,CNVrd2: no visible global function definition for ‘rect’
plotCNVrd2,CNVrd2: no visible global function definition for ‘text’
plotCNVrd2,CNVrd2: no visible global function definition for ‘lines’
plotCNVrd2,CNVrd2: no visible global function definition for ‘abline’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘ggplot’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘geom_line’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘aes’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘x1’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘x2’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘Quantile’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘coord_cartesian’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘theme’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘ylab’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘geom_rect’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘xmin’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘xmax’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘ymin’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘ymax’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘geom_text’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘x’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘y’
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
  ‘label’
plotPolymorphicRegion,CNVrd2: no visible global function definition for
  ‘grid.arrange’
segmentSamples,CNVrd2 : runFunction: no visible global function
  definition for ‘as’
segmentSamplesUsingPopInformation,CNVrd2: no visible global function
  definition for ‘fitted’
segmentSamplesUsingPopInformation,CNVrd2: no visible global function
  definition for ‘lm’
Undefined global functions or variables:
  GRanges Hsapiens Quantile ScanBamParam TabixFile abline aes
  alphabetFrequency as axis chisq.test coda.samples coord_cartesian
  countBam dnorm fisher.test fitted geno geom_line geom_rect geom_text
  ggplot grid.arrange hist jags.model kmeans label lines lm mclapply
  objectCNVrd2 p.adjust par plot readDNAStringSet readVcf rect text
  theme unmasked update write.table x x1 x2 xmax xmin y ylab ymax ymin
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "lines", "par",
             "plot", "rect", "text")
  importFrom("methods", "as")
  importFrom("stats", "chisq.test", "dnorm", "fisher.test", "fitted",
             "kmeans", "lm", "p.adjust", "update")
  importFrom("utils", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 4.82  0.255   5.277
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/CNVrd2.Rcheck/00check.log’
for details.



Installation output

CNVrd2.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNVrd2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CNVrd2’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNVrd2)

Tests output


Example timings

CNVrd2.Rcheck/CNVrd2-Ex.timings

nameusersystemelapsed
CNVrd2-class0.0020.0000.002
calculateLDSNPandCNV4.8200.2555.277
clusteringCNVs-class0.0020.0000.001
countReadInWindow-methods0.0000.0010.000
countReadInWindow0.0000.0000.001
emnormalCNV0.1650.0050.172
groupBayesianCNVs0.0010.0010.001
groupCNVs0.4060.0050.415
identifyPolymorphicRegion0.0000.0000.001
plotCNVrd20.1170.0050.121
plotPolymorphicRegion0.0000.0000.001
segmentSamples0.0080.0020.011