CNVrd2 1.8.0
Hoang Tan Nguyen
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CNVrd2 | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNVrd2_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CNVrd2.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [25s/26s] 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 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:
‘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 : .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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/22s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
calculateLDSNPandCNV 4.919 2.679 7.742
* 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-3.2-bioc/meat/CNVrd2.Rcheck/00check.log’
for details.