Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-15 11:05:46 -0500 (Sat, 15 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4160
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CNVrd2 on nebbiolo1


To the developers/maintainers of the CNVrd2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVrd2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 360/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVrd2 1.33.0  (landing page)
Hoang Tan Nguyen
Snapshot Date: 2022-01-14 13:55:18 -0500 (Fri, 14 Jan 2022)
git_url: https://git.bioconductor.org/packages/CNVrd2
git_branch: master
git_last_commit: 94f9538
git_last_commit_date: 2021-10-26 12:10:56 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNVrd2
Version: 1.33.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNVrd2.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNVrd2_1.33.0.tar.gz
StartedAt: 2022-01-14 18:41:25 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 18:45:04 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 219.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVrd2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNVrd2.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNVrd2_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CNVrd2.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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 ‘1.33.0’
* 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 ‘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
  ‘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 ‘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 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",
             "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 ... 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/CNVrd2.Rcheck/00check.log’
for details.



Installation output

CNVrd2.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CNVrd2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘CNVrd2’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNVrd2)

Tests output


Example timings

CNVrd2.Rcheck/CNVrd2-Ex.timings

nameusersystemelapsed
CNVrd2-class0.0010.0000.002
calculateLDSNPandCNV4.6310.1684.802
clusteringCNVs-class0.0010.0000.001
countReadInWindow-methods000
countReadInWindow0.0000.0010.000
emnormalCNV0.0800.0150.095
groupBayesianCNVs0.0000.0010.001
groupCNVs0.1820.0010.184
identifyPolymorphicRegion0.0000.0000.001
plotCNVrd20.0710.0040.075
plotPolymorphicRegion0.0010.0000.000
segmentSamples0.0020.0040.006