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BioC 3.5: CHECK report for intansv on tokay2

This page was generated on 2017-08-16 13:22:30 -0400 (Wed, 16 Aug 2017).

Package 674/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
intansv 1.14.0
Wen Yao
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/intansv
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: intansv
Version: 1.14.0
Command: rm -rf intansv.buildbin-libdir intansv.Rcheck && mkdir intansv.buildbin-libdir intansv.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=intansv.buildbin-libdir intansv_1.14.0.tar.gz >intansv.Rcheck\00install.out 2>&1 && cp intansv.Rcheck\00install.out intansv-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=intansv.buildbin-libdir --install="check:intansv-install.out" --force-multiarch --no-vignettes --timings intansv_1.14.0.tar.gz
StartedAt: 2017-08-16 00:38:46 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:50:06 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 680.8 seconds
RetCode: 0
Status:  OK  
CheckDir: intansv.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf intansv.buildbin-libdir intansv.Rcheck && mkdir intansv.buildbin-libdir intansv.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=intansv.buildbin-libdir intansv_1.14.0.tar.gz >intansv.Rcheck\00install.out 2>&1 && cp intansv.Rcheck\00install.out intansv-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=intansv.buildbin-libdir --install="check:intansv-install.out" --force-multiarch --no-vignettes --timings intansv_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/intansv.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.14.0'
* 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  5.9Mb
  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 '.hasSlot'
svAnnotation: no visible global function definition for 'queryHits'
svAnnotation: no visible global function definition for 'subjectHits'
Undefined global functions or variables:
  .hasSlot aes aes_string as.dist cutree ggplot hclust queryHits
  read.table seqlengths seqlengths<- subjectHits
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "as.dist", "cutree", "hclust")
  importFrom("utils", "read.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 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   18.86   0.00   18.86
geneAnnotation 16.75   0.47   17.22
plotChromosome  5.97   0.01    5.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
methodsMerge   125.79   0.01  125.82
geneAnnotation  18.66   0.25   18.91
plotChromosome   6.74   0.00    6.73
svAnnotation     5.72   0.00    5.71
plotRegion       5.47   0.00    5.47
readLumpy        5.47   0.00    5.47
readDelly        5.14   0.00    5.14
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/intansv.Rcheck/00check.log'
for details.


intansv.Rcheck/00install.out:


install for i386

* installing *source* package 'intansv' ...
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'intansv' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'intansv' as intansv_1.14.0.zip
* DONE (intansv)

intansv.Rcheck/examples_i386/intansv-Ex.timings:

nameusersystemelapsed
geneAnnotation16.75 0.4717.22
methodsMerge18.86 0.0018.86
plotChromosome5.970.015.99
plotRegion4.240.034.26
readBreakDancer2.710.002.72
readCnvnator0.660.000.66
readDelly3.340.003.34
readLumpy2.720.002.72
readPindel2.840.002.84
readSoftSearch0.280.000.28
readSvseq0.640.000.64
svAnnotation4.370.024.40

intansv.Rcheck/examples_x64/intansv-Ex.timings:

nameusersystemelapsed
geneAnnotation18.66 0.2518.91
methodsMerge125.79 0.01125.82
plotChromosome6.740.006.73
plotRegion5.470.005.47
readBreakDancer3.310.023.33
readCnvnator0.670.000.67
readDelly5.140.005.14
readLumpy5.470.005.47
readPindel3.150.003.15
readSoftSearch0.330.000.33
readSvseq0.890.020.91
svAnnotation5.720.005.71