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BioC 3.2: CHECK report for BubbleTree on moscato1

This page was generated on 2016-04-23 10:21:26 -0700 (Sat, 23 Apr 2016).

Package 126/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.0.1
Wei Zhu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BubbleTree
Last Changed Rev: 113112 / Revision: 116712
Last Changed Date: 2016-01-30 16:29:21 -0800 (Sat, 30 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BubbleTree
Version: 2.0.1
Command: rm -rf BubbleTree.buildbin-libdir BubbleTree.Rcheck && mkdir BubbleTree.buildbin-libdir BubbleTree.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BubbleTree.buildbin-libdir BubbleTree_2.0.1.tar.gz >BubbleTree.Rcheck\00install.out 2>&1 && cp BubbleTree.Rcheck\00install.out BubbleTree-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BubbleTree.buildbin-libdir --install="check:BubbleTree-install.out" --force-multiarch --no-vignettes --timings BubbleTree_2.0.1.tar.gz
StartedAt: 2016-04-23 00:11:04 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:21:19 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 614.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BubbleTree.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BubbleTree.buildbin-libdir BubbleTree.Rcheck && mkdir BubbleTree.buildbin-libdir BubbleTree.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BubbleTree.buildbin-libdir BubbleTree_2.0.1.tar.gz >BubbleTree.Rcheck\00install.out 2>&1 && cp BubbleTree.Rcheck\00install.out BubbleTree-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BubbleTree.buildbin-libdir --install="check:BubbleTree-install.out" --force-multiarch --no-vignettes --timings BubbleTree_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/BubbleTree.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BubbleTree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BubbleTree' version '2.0.1'
* 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 'BubbleTree' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'BubbleTree'
  Warning: replacing previous import 'BiocGenerics::combine' by 'gridExtra::combine' when loading 'BubbleTree'
See 'D:/biocbld/bbs-3.2-bioc/meat/BubbleTree.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 24.1Mb
  sub-directories of 1Mb or more:
    data  22.7Mb
    doc    1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
It is recommended to use 'given' instead of 'middle'.
* 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [48s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
heteroLociTrack 7.05   0.19    7.27
btpredict       5.74   0.00    5.74
saveXLS         0.19   0.00    6.76
** running examples for arch 'x64' ... [47s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
heteroLociTrack 8.72   0.27    8.98
info            5.90   0.03    5.93
btpredict       5.71   0.05    5.79
* 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: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/BubbleTree.Rcheck/00check.log'
for details.


BubbleTree.Rcheck/00install.out:


install for i386

* installing *source* package 'BubbleTree' ...
It is recommended to use 'given' instead of 'middle'.
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'BubbleTree'
Warning: replacing previous import 'BiocGenerics::combine' by 'gridExtra::combine' when loading 'BubbleTree'
Found more than one class "GenomicRanges" in cache; using the first, from namespace 'GenomicRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'BubbleTree'
Warning: replacing previous import 'BiocGenerics::combine' by 'gridExtra::combine' when loading 'BubbleTree'

install for x64

* installing *source* package 'BubbleTree' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'BubbleTree'
Warning: replacing previous import 'BiocGenerics::combine' by 'gridExtra::combine' when loading 'BubbleTree'
* MD5 sums
packaged installation of 'BubbleTree' as BubbleTree_2.0.1.zip
* DONE (BubbleTree)

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

nameusersystemelapsed
Annotate000
BTreePlotter0.110.000.11
BTreePredictor0.020.000.01
RscoreTrack1.190.031.22
TrackPlotter000
annoByGenesAndCyto1.340.021.36
bafTrack0.330.000.33
btcompare0.020.000.02
btpredict5.740.005.74
drawBTree0.440.000.44
drawBubbles0.440.020.45
drawFeatures1.840.031.94
getTracks0.760.010.78
heteroLociTrack7.050.197.27
info4.250.004.24
loadRBD0.090.000.09
saveXLS0.190.006.76
trackBTree0.400.020.42
xyTrack0.280.000.28

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

nameusersystemelapsed
Annotate000
BTreePlotter0.140.000.93
BTreePredictor0.010.000.01
RscoreTrack0.490.000.49
TrackPlotter000
annoByGenesAndCyto1.340.001.34
bafTrack0.340.000.34
btcompare000
btpredict5.710.055.79
drawBTree0.330.000.33
drawBubbles0.390.000.39
drawFeatures1.570.001.57
getTracks1.560.011.58
heteroLociTrack8.720.278.98
info5.900.035.93
loadRBD0.090.000.09
saveXLS0.170.013.07
trackBTree0.50.00.5
xyTrack0.330.000.33