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‎revdep/README.md‎

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# Setup
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## Platform
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|setting |value |
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|:--------|:--------------------------------------|
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|version |R version 3.3.2 RC (2016-10-26 r71594) |
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|system |x86_64, darwin13.4.0 |
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|ui |X11 |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|tz |America/New_York |
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|date |2017-04-20 |
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## Packages
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|package |* |version |date |source |
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|:--------|:--|:----------|:----------|:--------------------------------|
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|aws.s3 | |0.2.2 |2017-04-20 |Github (cloudyr/aws.s3@305e9da) |
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|covr | |2.2.2 |2017-04-20 |Github (jimhester/covr@accef86) |
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|digest | |0.6.12 |2017-01-27 |cran (@0.6.12) |
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|httr | |1.2.1 |2016-07-03 |cran (@1.2.1) |
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|memoise | |1.0.0 |2016-01-29 |cran (@1.0.0) |
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|testthat | |1.0.2.9000 |2017-03-03 |Github (hadley/testthat@b72a228) |
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# Check results
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21 packages
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|package |version | errors| warnings| notes|
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|:--------------|:-------|------:|--------:|-----:|
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|biolink |0.1.2 | 1| 0| 0|
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|BWStest |0.2.1 | 0| 0| 0|
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|covr |2.2.2 | 0| 0| 0|
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|devtools |1.12.0 | 0| 0| 0|
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|functools |0.2.0 | 0| 0| 0|
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|GSED |1.3 | 0| 0| 0|
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|gWidgets2RGtk2 |1.0-5 | 1| 0| 0|
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|gWidgets2tcltk |1.0-5 | 1| 0| 0|
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|heemod |0.9.0 | 0| 0| 0|
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|icd9 |1.3.1 | 0| 0| 1|
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|opencage |0.1.0 | 0| 0| 0|
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|OpenML |1.3 | 0| 0| 0|
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|prcbench |0.7.3 | 0| 0| 1|
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|regioneR |1.6.2 | 0| 1| 4|
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|rgho |1.0.1 | 0| 0| 0|
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|RSQLite |1.1-2 | 0| 0| 0|
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|saeRobust |0.1.0 | 0| 0| 0|
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|SamplingStrata |1.1 | 0| 0| 0|
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|SIDES |1.10 | 0| 0| 0|
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|surveillance |1.13.0 | 0| 0| 2|
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|toaster |0.5.5 | 0| 0| 0|
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## biolink (0.1.2)
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Maintainer: Aaron Wolen <[email protected]>
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1 error | 0 warnings | 0 notes
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```
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checking tests ... ERROR
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Running the tests in ‘tests/testthat.R’ failed.
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Last 13 lines of output:
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}) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:28
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18: FUN(X[[i]], ...)
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19: codetools::findFuncLocals(formals(fun), body(fun)) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:53
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20: findLocalsList(c(list(body), dropMissings(formals)))
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21: body(fun)
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22: get(fun, mode = "function", envir = parent.frame())
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testthat results ================================================================
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OK: 138 SKIPPED: 0 FAILED: 1
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1. Error: Package Style (@test-style.r#4)
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Error: testthat unit tests failed
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Execution halted
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```
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## BWStest (0.2.1)
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Maintainer: Steven E. Pav <[email protected]>
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Bug reports: https://github.com/shabbychef/BWStest/issues
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0 errors | 0 warnings | 0 notes
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## covr (2.2.2)
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Maintainer: Jim Hester <[email protected]>
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Bug reports: https://github.com/jimhester/covr/issues
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0 errors | 0 warnings | 0 notes
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## devtools (1.12.0)
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Maintainer: Hadley Wickham <[email protected]>
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Bug reports: https://github.com/hadley/devtools/issues
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0 errors | 0 warnings | 0 notes
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## functools (0.2.0)
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Maintainer: Paul Hendricks <[email protected]>
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Bug reports: https://github.com/paulhendricks/functools/issues
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0 errors | 0 warnings | 0 notes
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## GSED (1.3)
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Maintainer: Marie-Karelle Riviere <[email protected]>
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0 errors | 0 warnings | 0 notes
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## gWidgets2RGtk2 (1.0-5)
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Maintainer: John Verzani <[email protected]>
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1 error | 0 warnings | 0 notes
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```
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checking package dependencies ... ERROR
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Package required but not available: ‘RGtk2’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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manual.
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```
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## gWidgets2tcltk (1.0-5)
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Maintainer: John Verzani <[email protected]>
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1 error | 0 warnings | 0 notes
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```
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checking whether package ‘gWidgets2tcltk’ can be installed ... ERROR
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Installation failed.
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See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/gWidgets2tcltk.Rcheck/00install.out’ for details.
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```
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## heemod (0.9.0)
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Maintainer: Antoine Filipovic-Pierucci <[email protected]>
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Bug reports: https://github.com/pierucci/heemod/issues
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0 errors | 0 warnings | 0 notes
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## icd9 (1.3.1)
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Maintainer: Jack O. Wasey <[email protected]>
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Bug reports: https://github.com/jackwasey/icd9/issues
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0 errors | 0 warnings | 1 note
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```
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checking dependencies in R code ... NOTE
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Missing or unexported object: ‘devtools::load_data’
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```
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## opencage (0.1.0)
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Maintainer: Maëlle Salmon <[email protected]>
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Bug reports: http://github.com/ropenscilabs/opencage/issues
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0 errors | 0 warnings | 0 notes
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## OpenML (1.3)
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Maintainer: Giuseppe Casalicchio <[email protected]>
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Bug reports: https://github.com/openml/openml-r/issues
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0 errors | 0 warnings | 0 notes
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## prcbench (0.7.3)
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Maintainer: Takaya Saito <[email protected]>
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Bug reports: https://github.com/takayasaito/prcbench/issues
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0 errors | 0 warnings | 1 note
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```
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checking package dependencies ... NOTE
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Package suggested but not available for checking: ‘PerfMeas’
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```
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## regioneR (1.6.2)
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Maintainer: Bernat Gel <[email protected]>
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0 errors | 1 warning | 4 notes
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```
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checking whether package ‘regioneR’ can be installed ... WARNING
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Found the following significant warnings:
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Warning: package ‘S4Vectors’ was built under R version 3.3.3
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Warning: package ‘IRanges’ was built under R version 3.3.3
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See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00install.out’ for details.
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checking DESCRIPTION meta-information ... NOTE
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Packages listed in more than one of Depends, Imports, Suggests, Enhances:
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‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
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A package should be listed in only one of these fields.
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checking S3 generic/method consistency ... NOTE
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Found the following apparent S3 methods exported but not registered:
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print.permTestResults
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See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
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manual.
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checking R code for possible problems ... NOTE
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commonRegions: no visible global function definition for ‘hasArg’
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(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:38)
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commonRegions: no visible global function definition for ‘hasArg’
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(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:39)
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createFunctionsList: no visible global function definition for ‘hasArg’
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(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:47)
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createFunctionsList: no visible global function definition for ‘hasArg’
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(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:48)
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createFunctionsList: no visible global function definition for ‘hasArg’
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... 109 lines ...
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uniqueRegions: no visible global function definition for ‘hasArg’
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(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:37)
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uniqueRegions: no visible global function definition for ‘hasArg’
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(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:38)
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Undefined global functions or variables:
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hasArg is queryHits read.csv read.delim subjectHits
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Consider adding
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importFrom("methods", "hasArg", "is")
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importFrom("utils", "read.csv", "read.delim")
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to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
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contains 'methods').
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checking Rd line widths ... NOTE
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Rd file 'circularRandomizeRegions.Rd':
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\usage lines wider than 90 characters:
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circularRandomizeRegions(A, genome="hg19", mask=NULL, max.mask.overlap=NULL, max.retries=10, verbose=TRUE, ...)
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Rd file 'commonRegions.Rd':
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\examples lines wider than 100 characters:
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plotRegions(list(A, B, commons), chromosome="chr1", regions.labels=c("A", "B", "common"), regions.colors=3:1)
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Rd file 'createFunctionsList.Rd':
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... 95 lines ...
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plotRegions(list(A, B, splits), chromosome=1, regions.labels=c("A", "B", "splits"), regions.colors=3:1)
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Rd file 'subtractRegions.Rd':
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\examples lines wider than 100 characters:
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plotRegions(list(A, B, subtract), chromosome=1, regions.labels=c("A", "B", "subtract"), regions.colors=3:1)
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Rd file 'uniqueRegions.Rd':
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\examples lines wider than 100 characters:
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plotRegions(list(A, B, uniques), chromosome="chr1", regions.labels=c("A", "B", "uniques"), regions.colors=3:1)
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These lines will be truncated in the PDF manual.
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```
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## rgho (1.0.1)
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Maintainer: Antoine Filipovic-Pierucci <[email protected]>
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Bug reports: https://github.com/pierucci/rgho/issues
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0 errors | 0 warnings | 0 notes
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## RSQLite (1.1-2)
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Maintainer: Kirill Müller <[email protected]>
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Bug reports: https://github.com/rstats-db/RSQLite/issues
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0 errors | 0 warnings | 0 notes
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## saeRobust (0.1.0)
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Maintainer: Sebastian Warnholz <[email protected]>
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Bug reports: https://github.com/wahani/saeRobust/issues
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0 errors | 0 warnings | 0 notes
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## SamplingStrata (1.1)
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Maintainer: Giulio Barcaroli <[email protected]>
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0 errors | 0 warnings | 0 notes
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## SIDES (1.10)
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Maintainer: Marie-Karelle Riviere <[email protected]>
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0 errors | 0 warnings | 0 notes
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## surveillance (1.13.0)
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Maintainer: Sebastian Meyer <[email protected]>
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Bug reports: https://r-forge.r-project.org/tracker/?group_id=45
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0 errors | 0 warnings | 2 notes
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```
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checking package dependencies ... NOTE
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Package suggested but not available for checking: ‘INLA’
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checking installed package size ... NOTE
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installed size is 9.6Mb
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sub-directories of 1Mb or more:
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R 4.2Mb
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doc 2.3Mb
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```
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## toaster (0.5.5)
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Maintainer: Gregory Kanevsky <[email protected]>
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Bug reports: https://github.com/teradata-aster-field/toaster/issues
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0 errors | 0 warnings | 0 notes
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‎revdep/check.R‎

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library("devtools")
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res <- revdep_check(bioconductor = TRUE, threads = 4)
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revdep_check_save_summary(res)
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revdep_check_save_logs(res)
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revdep_check_resume(bioconductor = TRUE)
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revdep_check_save_summary()
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revdep_check_print_problems()

‎revdep/checks.rds‎

4.82 KB
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