intansv 1.10.0
Wen Yao
| 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/intansv | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 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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### rm -rf intansv.buildbin-libdir intansv.Rcheck && mkdir intansv.buildbin-libdir intansv.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=intansv.buildbin-libdir intansv_1.10.0.tar.gz >intansv.Rcheck\00install.out 2>&1 && cp intansv.Rcheck\00install.out intansv-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=intansv.buildbin-libdir --install="check:intansv-install.out" --force-multiarch --no-vignettes --timings intansv_1.10.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/intansv.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'intansv/DESCRIPTION' ... OK
* this is package 'intansv' version '1.10.0'
* 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 'intansv' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
extdata 5.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
LumpyCluster: no visible global function definition for 'subjectHits'
PindelCluster: no visible global function definition for 'subjectHits'
breakDancerCluster: no visible global function definition for
'subjectHits'
dellyCluster: no visible global function definition for 'subjectHits'
geneAnnotation: no visible global function definition for 'queryHits'
geneAnnotation: no visible global function definition for 'subjectHits'
methodsCluster: no visible global function definition for 'hclust'
methodsCluster: no visible global function definition for 'as.dist'
methodsCluster: no visible global function definition for 'cutree'
methodsMerge: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for 'queryHits'
plotChromosome: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for
'seqlengths<-'
plotChromosome: no visible global function definition for 'seqlengths'
plotChromosome: no visible global function definition for 'ggplot'
plotChromosome: no visible global function definition for 'aes'
plotRegion: no visible global function definition for 'seqlengths<-'
plotRegion: no visible global function definition for 'ggplot'
plotRegion: no visible global function definition for 'subjectHits'
plotRegion: no visible global function definition for 'aes_string'
readBreakDancer: no visible global function definition for 'read.table'
readBreakDancer: no visible global function definition for
'subjectHits'
readCnvnator : <anonymous>: no visible global function definition for
'read.table'
readCnvnator: no visible global function definition for 'subjectHits'
readDelly : <anonymous>: no visible global function definition for
'read.table'
readDelly: no visible global function definition for 'subjectHits'
readLumpy: no visible global function definition for 'read.table'
readLumpy: no visible global function definition for 'subjectHits'
readPindel : <anonymous>: no visible global function definition for
'read.table'
readPindel: no visible global function definition for 'subjectHits'
readSoftSearch: no visible global function definition for 'read.table'
readSoftSearch: no visible global function definition for 'subjectHits'
readSvseq : <anonymous>: no visible global function definition for
'read.table'
readSvseq: no visible global function definition for 'subjectHits'
readSvseq : <anonymous>: no visible global function definition for
'subjectHits'
softSearchCluster: no visible global function definition for
'subjectHits'
svAnnotation: no visible global function definition for 'queryHits'
svAnnotation: no visible global function definition for 'subjectHits'
Undefined global functions or variables:
aes aes_string as.dist cutree ggplot hclust queryHits read.table
seqlengths seqlengths<- subjectHits
Consider adding
importFrom("stats", "as.dist", "cutree", "hclust")
importFrom("utils", "read.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
methodsMerge 30.30 0.00 30.30
geneAnnotation 24.82 0.14 24.97
svAnnotation 7.37 0.00 7.39
plotChromosome 6.99 0.02 7.05
plotRegion 6.55 0.01 6.60
readDelly 6.02 0.00 6.02
readLumpy 5.12 0.00 5.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
methodsMerge 40.56 0.03 40.60
geneAnnotation 33.67 0.35 34.02
svAnnotation 9.03 0.02 9.05
plotChromosome 9.01 0.01 9.03
plotRegion 8.51 0.00 8.50
readDelly 6.67 0.00 6.66
readLumpy 5.86 0.00 5.86
readBreakDancer 5.83 0.00 5.85
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'rtracklayer'
* 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-3.3-bioc/meat/intansv.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'intansv' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
install for x64
* installing *source* package 'intansv' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* MD5 sums
packaged installation of 'intansv' as intansv_1.10.0.zip
* DONE (intansv)