revdep/problems.md

Setup

Platform

|setting |value | |:--------|:--------------------------------------| |version |R version 3.3.2 RC (2016-10-26 r71594) | |system |x86_64, darwin13.4.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/New_York | |date |2017-04-20 |

Packages

|package |* |version |date |source | |:--------|:--|:----------|:----------|:--------------------------------| |aws.s3 | |0.2.2 |2017-04-20 |Github (cloudyr/[email protected]) | |covr | |2.2.2 |2017-04-20 |Github (jimhester/[email protected]) | |digest | |0.6.12 |2017-01-27 |cran (@0.6.12) | |httr | |1.2.1 |2016-07-03 |cran (@1.2.1) | |memoise | |1.0.0 |2016-01-29 |cran (@1.0.0) | |testthat | |1.0.2.9000 |2017-03-03 |Github (hadley/[email protected]) |

Check results

4 packages with problems

|package |version | errors| warnings| notes| |:--------------|:-------|------:|--------:|-----:| |biolink |0.1.2 | 1| 0| 0| |gWidgets2RGtk2 |1.0-5 | 1| 0| 0| |gWidgets2tcltk |1.0-5 | 1| 0| 0| |regioneR |1.6.2 | 0| 1| 4|

biolink (0.1.2)

Maintainer: Aaron Wolen [email protected]

1 error | 0 warnings | 0 notes

checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     }) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:28
  18: FUN(X[[i]], ...)
  19: codetools::findFuncLocals(formals(fun), body(fun)) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:53
  20: findLocalsList(c(list(body), dropMissings(formals)))
  21: body(fun)
  22: get(fun, mode = "function", envir = parent.frame())

  testthat results ================================================================
  OK: 138 SKIPPED: 0 FAILED: 1
  1. Error: Package Style (@test-style.r#4) 

  Error: testthat unit tests failed
  Execution halted

gWidgets2RGtk2 (1.0-5)

Maintainer: John Verzani [email protected]

1 error | 0 warnings | 0 notes

checking package dependencies ... ERROR
Package required but not available: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

gWidgets2tcltk (1.0-5)

Maintainer: John Verzani [email protected]

1 error | 0 warnings | 0 notes

checking whether package ‘gWidgets2tcltk’ can be installed ... ERROR
Installation failed.
See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/gWidgets2tcltk.Rcheck/00install.out’ for details.

regioneR (1.6.2)

Maintainer: Bernat Gel [email protected]

0 errors | 1 warning | 4 notes

checking whether package ‘regioneR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.3.3
  Warning: package ‘IRanges’ was built under R version 3.3.3
See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00install.out’ for details.

checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
A package should be listed in only one of these fields.

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.permTestResults
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
commonRegions: no visible global function definition for ‘hasArg’
  (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:38)
commonRegions: no visible global function definition for ‘hasArg’
  (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:39)
createFunctionsList: no visible global function definition for ‘hasArg’
  (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:47)
createFunctionsList: no visible global function definition for ‘hasArg’
  (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:48)
createFunctionsList: no visible global function definition for ‘hasArg’
... 109 lines ...
uniqueRegions: no visible global function definition for ‘hasArg’
  (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:37)
uniqueRegions: no visible global function definition for ‘hasArg’
  (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:38)
Undefined global functions or variables:
  hasArg is queryHits read.csv read.delim subjectHits
Consider adding
  importFrom("methods", "hasArg", "is")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

checking Rd line widths ... NOTE
Rd file 'circularRandomizeRegions.Rd':
  \usage lines wider than 90 characters:
     circularRandomizeRegions(A, genome="hg19", mask=NULL, max.mask.overlap=NULL, max.retries=10, verbose=TRUE, ...)

Rd file 'commonRegions.Rd':
  \examples lines wider than 100 characters:
     plotRegions(list(A, B, commons), chromosome="chr1", regions.labels=c("A", "B", "common"), regions.colors=3:1)

Rd file 'createFunctionsList.Rd':
... 95 lines ...
     plotRegions(list(A, B, splits), chromosome=1, regions.labels=c("A", "B", "splits"), regions.colors=3:1)

Rd file 'subtractRegions.Rd':
  \examples lines wider than 100 characters:
     plotRegions(list(A, B, subtract), chromosome=1, regions.labels=c("A", "B", "subtract"), regions.colors=3:1)

Rd file 'uniqueRegions.Rd':
  \examples lines wider than 100 characters:
     plotRegions(list(A, B, uniques), chromosome="chr1", regions.labels=c("A", "B", "uniques"), regions.colors=3:1)

These lines will be truncated in the PDF manual.


hadley/memoise documentation built on March 26, 2018, 10:56 a.m.