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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVrd2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVrd2_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CNVrd2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVrd2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVrd2’ version ‘1.42.0’
* 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 code 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:
‘ggplot2’ ‘gridExtra’ ‘methods’ ‘parallel’ ‘rjags’
‘VariantAnnotation’
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:
abline aes alphabetFrequency as axis chisq.test coda.samples
coord_cartesian countBam dnorm fisher.test fitted geno geom_line
geom_rect geom_text ggplot GRanges grid.arrange hist Hsapiens
jags.model kmeans label lines lm mclapply objectCNVrd2 p.adjust par
Quantile readDNAStringSet readVcf rect ScanBamParam TabixFile 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 ... NOTE
checkRd: (-1) identifyPolymorphicRegion.Rd:15-16: Lost braces
15 | \code{polymorphicRegionObject}{An object obtained from the process of
| ^
checkRd: (-1) plotPolymorphicRegion.Rd:18-19: Lost braces
18 | \code{polymorphicRegionObject}{An object obtained from the process of
| ^
* 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CNVrd2.Rcheck/00check.log’
for details.
