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BioC 3.1: CHECK report for CNVrd2 on moscato2

This page was generated on 2015-10-09 09:30:49 -0700 (Fri, 09 Oct 2015).

Package 192/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVrd2 1.6.0
Hoang Tan Nguyen
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CNVrd2
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: CNVrd2
Version: 1.6.0
Command: rm -rf CNVrd2.buildbin-libdir CNVrd2.Rcheck && mkdir CNVrd2.buildbin-libdir CNVrd2.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNVrd2.buildbin-libdir CNVrd2_1.6.0.tar.gz >CNVrd2.Rcheck\00install.out 2>&1 && cp CNVrd2.Rcheck\00install.out CNVrd2-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CNVrd2.buildbin-libdir --install="check:CNVrd2-install.out" --force-multiarch --no-vignettes --timings CNVrd2_1.6.0.tar.gz
StartedAt: 2015-10-09 00:35:05 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:39:52 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 286.5 seconds
RetCode: 0
Status:  OK  
CheckDir: CNVrd2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNVrd2.buildbin-libdir CNVrd2.Rcheck && mkdir CNVrd2.buildbin-libdir CNVrd2.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNVrd2.buildbin-libdir CNVrd2_1.6.0.tar.gz >CNVrd2.Rcheck\00install.out 2>&1 && cp CNVrd2.Rcheck\00install.out CNVrd2-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CNVrd2.buildbin-libdir --install="check:CNVrd2-install.out" --force-multiarch --no-vignettes --timings CNVrd2_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/CNVrd2.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.6.0'
* 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 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 : .local: warning in matrix(0, nr =
  length(x2), ncol = k - 2): partial argument match of 'nr' to 'nrow'
segmentSamples,CNVrd2 : .local: 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'
groupBayesianCNVs: no visible global function definition for
  'jags.model'
groupBayesianCNVs: no visible global function definition for
  'coda.samples'
countReadInWindow,CNVrd2 : .local: no visible global function
  definition for 'readDNAStringSet'
countReadInWindow,CNVrd2 : .local: no visible binding for global
  variable 'objectCNVrd2'
countReadInWindow,CNVrd2 : .local: no visible global function
  definition for 'ScanBamParam'
countReadInWindow,CNVrd2 : .local : <anonymous>: no visible global
  function definition for 'countBam'
countReadInWindow,CNVrd2 : .local : gcContent: no visible global
  function definition for 'unmasked'
countReadInWindow,CNVrd2 : .local : gcContent: no visible binding for
  global variable 'Hsapiens'
countReadInWindow,CNVrd2 : .local : gcContent: no visible global
  function definition for 'alphabetFrequency'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'ggplot'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'geom_line'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'aes'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'x1'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'x2'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'Quantile'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'coord_cartesian'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'theme'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'ylab'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'geom_rect'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'xmin'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'xmax'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'ymin'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'ymax'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'geom_text'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'x'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'y'
plotPolymorphicRegion,CNVrd2 : .local: no visible binding for global
  variable 'label'
plotPolymorphicRegion,CNVrd2 : .local: no visible global function
  definition for 'grid.arrange'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [14s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 3.58   0.82    5.21
** running examples for arch 'x64' ... [17s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 4.62   0.92    5.54
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/CNVrd2.Rcheck/00check.log'
for details.


CNVrd2.Rcheck/00install.out:


install for i386

* installing *source* package 'CNVrd2' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'CNVrd2' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'CNVrd2' as CNVrd2_1.6.0.zip
* DONE (CNVrd2)

CNVrd2.Rcheck/examples_i386/CNVrd2-Ex.timings:

nameusersystemelapsed
CNVrd2-class000
calculateLDSNPandCNV3.580.825.21
clusteringCNVs-class000
countReadInWindow-methods000
countReadInWindow000
emnormalCNV0.090.000.09
groupBayesianCNVs000
groupCNVs0.110.000.11
identifyPolymorphicRegion000
plotCNVrd20.070.000.07
plotPolymorphicRegion000
segmentSamples0.010.000.01

CNVrd2.Rcheck/examples_x64/CNVrd2-Ex.timings:

nameusersystemelapsed
CNVrd2-class000
calculateLDSNPandCNV4.620.925.54
clusteringCNVs-class0.010.000.02
countReadInWindow-methods000
countReadInWindow000
emnormalCNV0.100.020.11
groupBayesianCNVs000
groupCNVs0.120.000.12
identifyPolymorphicRegion000
plotCNVrd20.060.000.06
plotPolymorphicRegion000
segmentSamples0.020.000.02