CNVrd2 1.10.2
Hoang Tan Nguyen
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/CNVrd2 | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | 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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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNVrd2_1.10.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CNVrd2.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.10.2’
* 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 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: 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
‘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’
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 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 write.table x x1 x2 xmax xmin y ylab ymax ymin
Consider adding
importFrom("graphics", "abline", "axis", "hist", "lines", "par",
"plot", "rect", "text")
importFrom("stats", "chisq.test", "dnorm", "fisher.test", "fitted",
"kmeans", "lm", "p.adjust")
importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calculateLDSNPandCNV 3.061 2.179 5.344
* 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-3.3-bioc/meat/CNVrd2.Rcheck/00check.log’
for details.