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BioC 3.0: CHECK report for intansv on moscato1

This page was generated on 2015-04-10 09:49:18 -0700 (Fri, 10 Apr 2015).

Package 458/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
intansv 1.6.2
Wen Yao
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/intansv
Last Changed Rev: 98675 / Revision: 102249
Last Changed Date: 2015-01-25 02:12:19 -0800 (Sun, 25 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
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 

Summary

Package: intansv
Version: 1.6.2
Command: rm -rf intansv.buildbin-libdir intansv.Rcheck && mkdir intansv.buildbin-libdir intansv.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=intansv.buildbin-libdir intansv_1.6.2.tar.gz >intansv.Rcheck\00install.out 2>&1 && cp intansv.Rcheck\00install.out intansv-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=intansv.buildbin-libdir --install="check:intansv-install.out" --force-multiarch --no-vignettes --timings intansv_1.6.2.tar.gz
StartedAt: 2015-04-10 02:22:47 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:36:27 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 820.7 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=intansv.buildbin-libdir intansv_1.6.2.tar.gz >intansv.Rcheck\00install.out 2>&1 && cp intansv.Rcheck\00install.out intansv-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=intansv.buildbin-libdir --install="check:intansv-install.out" --force-multiarch --no-vignettes --timings intansv_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/intansv.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'intansv/DESCRIPTION' ... OK
* this is package 'intansv' version '1.6.2'
* 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 whether package 'intansv' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
* 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
plotChromosome: no visible global function definition for
  'seqlengths<-'
plotChromosome: no visible global function definition for 'seqlengths'
plotChromosome: no visible global function definition for 'aes'
plotRegion: no visible global function definition for 'seqlengths<-'
plotRegion: no visible global function definition for 'aes_string'
* 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' ... [182s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
methodsMerge    48.91   0.01   48.92
geneAnnotation  36.19   0.28   36.47
plotChromosome  13.96   0.00   13.96
svAnnotation    13.62   0.00   13.62
plotRegion      12.85   0.02   12.87
readDelly       10.98   0.00   10.99
readBreakDancer  9.80   0.00    9.80
readLumpy        9.50   0.00    9.50
readPindel       8.16   0.00    8.16
** running examples for arch 'x64' ... [218s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
methodsMerge    55.62   0.02   55.65
geneAnnotation  42.88   0.20   43.09
plotRegion      17.05   0.01   17.06
plotChromosome  16.96   0.00   16.96
svAnnotation    15.10   0.00   15.10
readDelly       13.01   0.00   13.02
readLumpy       12.26   0.00   12.26
readBreakDancer 10.20   0.00   10.20
readPindel      10.04   0.00   10.05
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'intansv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'intansv' as intansv_1.6.2.zip
* DONE (intansv)

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

nameusersystemelapsed
geneAnnotation36.19 0.2836.47
methodsMerge48.91 0.0148.92
plotChromosome13.96 0.0013.96
plotRegion12.85 0.0212.87
readBreakDancer9.80.09.8
readCnvnator1.120.001.12
readDelly10.98 0.0010.99
readLumpy9.50.09.5
readPindel8.160.008.16
readSoftSearch0.760.000.76
readSvseq1.670.001.67
svAnnotation13.62 0.0013.62

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

nameusersystemelapsed
geneAnnotation42.88 0.2043.09
methodsMerge55.62 0.0255.65
plotChromosome16.96 0.0016.96
plotRegion17.05 0.0117.06
readBreakDancer10.2 0.010.2
readCnvnator1.060.001.06
readDelly13.01 0.0013.02
readLumpy12.26 0.0012.26
readPindel10.04 0.0010.05
readSoftSearch0.860.000.86
readSvseq2.500.002.49
svAnnotation15.1 0.015.1