BioC 3.3: CHECK report for epivizr on windows2.bioconductor.org

Package: epivizr

Version: 1.9.0

Command: rm -rf epivizr.buildbin-libdir epivizr.Rcheck && mkdir epivizr.buildbin-libdir epivizr.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epivizr.buildbin-libdir epivizr_1.9.0.tar.gz >epivizr.Rcheck\00install.out 2>&1 && cp epivizr.Rcheck\00install.out epivizr-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=epivizr.buildbin-libdir --install="check:epivizr-install.out" --force-multiarch --no-vignettes --timings epivizr_1.9.0.tar.gz

StartedAt: 2015-10-27 02:15:21 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:18:44 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 203.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: epivizr.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf epivizr.buildbin-libdir epivizr.Rcheck && mkdir epivizr.buildbin-libdir epivizr.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epivizr.buildbin-libdir epivizr_1.9.0.tar.gz >epivizr.Rcheck\00install.out 2>&1 && cp epivizr.Rcheck\00install.out epivizr-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=epivizr.buildbin-libdir --install="check:epivizr-install.out" --force-multiarch --no-vignettes --timings epivizr_1.9.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/epivizr.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'epivizr/DESCRIPTION' ... OK
* this is package 'epivizr' version '1.9.0'
* 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 'epivizr' can be installed ... OK
* checking installed package size ... OK
* 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
register,ExpressionSet: no visible global function definition for
  'IRanges'
Undefined global functions or variables:
  IRanges
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'EpivizBlockData-class.Rd':
  '[GenomicRanges]{GIntervalTree}'

Missing link or links in documentation object 'EpivizBpData-class.Rd':
  '[GenomicRanges]{GIntervalTree}'

Missing link or links in documentation object 'EpivizDeviceMgr-class.Rd':
  '[GenomicRanges]{GIntervalTree}'

Missing link or links in documentation object 'EpivizFeatureData-class.Rd':
  '[GenomicRanges]{GIntervalTree}'

Missing link or links in documentation object 'EpivizGeneInfoData-class.Rd':
  '[GenomicRanges]{GIntervalTree}'

Missing link or links in documentation object 'EpivizTrackDevice-class.Rd':
  '[GenomicRanges]{GIntervalTree}'

Missing link or links in documentation object 'register-methods.Rd':
  '[GenomicRanges]{GIntervalTree}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [7s] OK
* 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
  'c:/biocbld/bbs-3.3-bioc/meat/epivizr.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'epivizr' ...
** 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 'epivizr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epivizr' as epivizr_1.9.0.zip
* DONE (epivizr)

name	user	system	elapsed
EpivizDeviceMgr-class	0	0	0
EpivizServer-class	0	0	0
IndexedArray-class	0	0	0
Queue-class	0	0	0
makeGeneTrackAnnotation	0	0	0
startEpiviz	0	0	0
startStandalone	0	0	0
tcga_colon_example	0.12	0.00	0.13
tcga_colon_expression	0.36	0.00	0.36

name	user	system	elapsed
EpivizDeviceMgr-class	0	0	0
EpivizServer-class	0	0	0
IndexedArray-class	0.02	0.00	0.02
Queue-class	0	0	0
makeGeneTrackAnnotation	0.00	0.02	0.01
startEpiviz	0	0	0
startStandalone	0	0	0
tcga_colon_example	0.22	0.00	0.22
tcga_colon_expression	0.44	0.00	0.44