BioC 3.5: CHECK report for GenomicInteractions on tokay2

Package: GenomicInteractions

Version: 1.10.0

Command: rm -rf GenomicInteractions.buildbin-libdir GenomicInteractions.Rcheck && mkdir GenomicInteractions.buildbin-libdir GenomicInteractions.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicInteractions.buildbin-libdir GenomicInteractions_1.10.0.tar.gz >GenomicInteractions.Rcheck\00install.out 2>&1 && cp GenomicInteractions.Rcheck\00install.out GenomicInteractions-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicInteractions.buildbin-libdir --install="check:GenomicInteractions-install.out" --force-multiarch --no-vignettes --timings GenomicInteractions_1.10.0.tar.gz

StartedAt: 2017-10-18 00:05:18 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:16:22 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 663.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicInteractions.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf GenomicInteractions.buildbin-libdir GenomicInteractions.Rcheck && mkdir GenomicInteractions.buildbin-libdir GenomicInteractions.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicInteractions.buildbin-libdir GenomicInteractions_1.10.0.tar.gz >GenomicInteractions.Rcheck\00install.out 2>&1 && cp GenomicInteractions.Rcheck\00install.out GenomicInteractions-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicInteractions.buildbin-libdir --install="check:GenomicInteractions-install.out" --force-multiarch --no-vignettes --timings GenomicInteractions_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicInteractions.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicInteractions/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicInteractions' version '1.10.0'
* 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 'GenomicInteractions' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
  Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicInteractions.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   7.9Mb
* 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 ... 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' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
export.bed12     3.03   0.02    8.49
InteractionTrack 1.64   0.07   30.78
plotCisTrans     1.44   0.11    8.71
plotCounts       1.13   0.00    9.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
InteractionTrack 2.16   0.04    5.25
plotAvgViewpoint 0.34   0.00    6.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicInteractions.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GenomicInteractions' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
** 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 'GenomicInteractions'
Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'

install for x64

* installing *source* package 'GenomicInteractions' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
* MD5 sums
packaged installation of 'GenomicInteractions' as GenomicInteractions_1.10.0.zip
* DONE (GenomicInteractions)

name	user	system	elapsed
GInteractions-subsetByFeatures-methods	0.51	0.00	0.52
GenomicInteractions-class	0.25	0.00	0.25
GenomicInteractions-package	0	0	0
GenomicInteractions	0.21	0.00	0.20
InteractionHelpers	0.03	0.02	0.05
InteractionTrack	1.64	0.07	30.78
annotateInteractions	0.14	0.00	0.14
annotateRegions	0.04	0.01	0.05
asBED-GInteractions-method	0.29	0.02	0.31
availableDisplayPars	0.03	0.00	0.03
calculateDistances	0.04	0.00	0.04
categoriseInteractions	0.20	0.01	0.21
export.bed12	3.03	0.02	8.49
export.bedpe	0.36	0.02	4.29
export.chiasig	0.30	0.03	0.79
export.igraph	0.12	0.02	0.14
getters	0.09	0.00	0.10
makeGenomicInteractionsFromFile	2.41	0.03	2.43
plotAvgViewpoint	0.31	0.00	4.89
plotCisTrans	1.44	0.11	8.71
plotCounts	1.13	0.00	9.23
plotDists	0.25	0.00	0.25
plotInteractionAnnotations	0.67	0.01	0.69
plotSummaryStats	1	0	1
plotViewpoint	0.44	0.02	0.45
resetAnnotations	0.04	0.00	0.05
setters	0.03	0.00	0.03
summariseByFeaturePairs	0.93	0.03	0.95
summariseByFeatures	0.34	0.02	0.36
viewPoint	0.19	0.00	0.19

name	user	system	elapsed
GInteractions-subsetByFeatures-methods	0.7	0.0	0.7
GenomicInteractions-class	0.32	0.00	0.31
GenomicInteractions-package	0	0	0
GenomicInteractions	0.41	0.00	0.40
InteractionHelpers	0.04	0.02	0.06
InteractionTrack	2.16	0.04	5.25
annotateInteractions	0.15	0.00	0.15
annotateRegions	0.05	0.00	0.05
asBED-GInteractions-method	0.31	0.00	0.31
availableDisplayPars	0.03	0.00	0.03
calculateDistances	0.05	0.00	0.05
categoriseInteractions	0.25	0.00	0.25
export.bed12	3.68	0.00	3.69
export.bedpe	0.24	0.02	0.45
export.chiasig	0.20	0.03	0.23
export.igraph	0.09	0.00	0.10
getters	0.11	0.00	0.11
makeGenomicInteractionsFromFile	1.18	0.00	1.17
plotAvgViewpoint	0.34	0.00	6.89
plotCisTrans	1.65	0.02	1.66
plotCounts	1.82	0.00	1.83
plotDists	0.46	0.00	0.61
plotInteractionAnnotations	0.62	0.03	0.66
plotSummaryStats	1.2	0.0	1.2
plotViewpoint	0.85	0.02	0.86
resetAnnotations	0.05	0.01	0.06
setters	0.07	0.00	0.08
summariseByFeaturePairs	1.08	0.02	1.10
summariseByFeatures	0.41	0.00	0.40
viewPoint	0.28	0.01	0.30