Package: CNVrd2

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVrd2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CNVrd2_1.20.0.tar.gz

StartedAt: 2019-04-13 01:21:45 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:27:14 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 328.3 seconds

RetCode: 0

Status:  OK

CheckDir: CNVrd2.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVrd2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CNVrd2_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/CNVrd2.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/CNVrd2.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CNVrd2_1.20.0.tar.gz && rm -rf CNVrd2.buildbin-libdir && mkdir CNVrd2.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVrd2.buildbin-libdir CNVrd2_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CNVrd2_1.20.0.zip && rm CNVrd2_1.20.0.tar.gz CNVrd2_1.20.0.zip
###
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install for i386

* installing *source* package 'CNVrd2' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVrd2'
    finding HTML links ... done
    CNVrd2-class                            html  
    CNVrd2-package                          html  
    calculateLDSNPandCNV                    html  
    ccl3l1data                              html  
    clusteringCNVs-class                    html  
    countReadInWindow-methods               html  
    countReadInWindow                       html  
    emnormalCNV-methods                     html  
    emnormalCNV                             html  
    fcgr3bMXL                               html  
    groupBayesianCNVs                       html  
    groupCNVs-methods                       html  
    groupCNVs                               html  
    identifyPolymorphicRegion-methods       html  
    identifyPolymorphicRegion               html  
    numericOrNULL-class                     html  
    plotCNVrd2-methods                      html  
    plotCNVrd2                              html  
    plotPolymorphicRegion-methods           html  
    plotPolymorphicRegion                   html  
    searchGroupCNVs-methods                 html  
    searchGroupCNVs                         html  
    segmentSamples-methods                  html  
    segmentSamples                          html  
    segmentSamplesUsingPopInformation-methods
                                            html  
    segmentSamplesUsingPopInformation       html  
    vectorORfactor-class                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CNVrd2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVrd2' as CNVrd2_1.20.0.zip
* DONE (CNVrd2)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CNVrd2' successfully unpacked and MD5 sums checked
In R CMD INSTALL