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BioC 3.0: CHECK report for Gviz on moscato1

This page was generated on 2015-04-10 09:47:43 -0700 (Fri, 10 Apr 2015).

Package 413/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.10.11
Florian Hahne
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/Gviz
Last Changed Rev: 101202 / Revision: 102249
Last Changed Date: 2015-03-26 02:48:19 -0700 (Thu, 26 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: Gviz
Version: 1.10.11
Command: rm -rf Gviz.buildbin-libdir Gviz.Rcheck && mkdir Gviz.buildbin-libdir Gviz.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Gviz.buildbin-libdir Gviz_1.10.11.tar.gz >Gviz.Rcheck\00install.out 2>&1 && cp Gviz.Rcheck\00install.out Gviz-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Gviz.buildbin-libdir --install="check:Gviz-install.out" --force-multiarch --no-vignettes --timings Gviz_1.10.11.tar.gz
StartedAt: 2015-04-10 02:03:49 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:13:53 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 603.6 seconds
RetCode: 0
Status:  OK  
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Gviz.buildbin-libdir Gviz.Rcheck && mkdir Gviz.buildbin-libdir Gviz.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Gviz.buildbin-libdir Gviz_1.10.11.tar.gz >Gviz.Rcheck\00install.out 2>&1 && cp Gviz.Rcheck\00install.out Gviz-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Gviz.buildbin-libdir --install="check:Gviz-install.out" --force-multiarch --no-vignettes --timings Gviz_1.10.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/Gviz.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 'Gviz/DESCRIPTION' ... OK
* this is package 'Gviz' version '1.10.11'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'grid' 'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb'
  'GenomicRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'Gviz' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   2.1Mb
* 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
* 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 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
.findMismatches: no visible global function definition for
  'consensusString'
.moreInd: no visible global function definition for 'grid.polyline'
subseq,SequenceTrack: no visible global function definition for
  'unmasked'
subseq,SequenceTrack: no visible global function definition for
  'complement'
* 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' ... [72s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SequenceTrack-class   17.47   0.37   17.85
AlignmentsTrack       10.97   0.36   11.41
GeneRegionTrack-class  6.44   0.06    6.76
AnnotationTrack-class  5.44   0.05    5.49
GenomeAxisTrack-class  5.18   0.02    5.19
** running examples for arch 'x64' ... [91s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
SequenceTrack-class          20.41   0.49   20.89
AlignmentsTrack              13.78   0.50   14.36
GeneRegionTrack-class         8.46   0.08    9.86
AnnotationTrack-class         6.38   0.00    6.38
plotTracks                    6.19   0.00    6.22
GenomeAxisTrack-class         5.40   0.01    5.57
BiomartGeneRegionTrack-class  5.05   0.01    5.18
* 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 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/Gviz.Rcheck/00check.log'
for details.

Gviz.Rcheck/00install.out:


install for i386

* installing *source* package 'Gviz' ...
** R
** data
** 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 'Gviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Gviz' as Gviz_1.10.11.zip
* DONE (Gviz)

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

nameusersystemelapsed
AlignedReadTrack-class1.880.001.88
AlignmentsTrack10.97 0.3611.41
AnnotationTrack-class5.440.055.49
BiomartGeneRegionTrack-class3.560.003.56
DataTrack-class0.670.000.67
DisplayPars-class0.050.000.04
GeneRegionTrack-class6.440.066.76
GenomeAxisTrack-class5.180.025.19
IdeogramTrack-class0.390.000.39
SequenceTrack-class17.47 0.3717.85
plotTracks4.910.054.96

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

nameusersystemelapsed
AlignedReadTrack-class3.130.023.15
AlignmentsTrack13.78 0.5014.36
AnnotationTrack-class6.380.006.38
BiomartGeneRegionTrack-class5.050.015.18
DataTrack-class0.890.020.90
DisplayPars-class0.060.000.06
GeneRegionTrack-class8.460.089.86
GenomeAxisTrack-class5.400.015.57
IdeogramTrack-class0.680.000.69
SequenceTrack-class20.41 0.4920.89
plotTracks6.190.006.22