ivanek / Gviz

This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.
https://bioconductor.org/packages/Gviz/
Artistic License 2.0
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Missing dependency: xml2 #47

Closed HenrikBengtsson closed 3 years ago

HenrikBengtsson commented 3 years ago

Hi, it looks like xml2 needs to be added to Suggests, or alternatively test conditionally on requireNamespace("xml2"). I spotted this while running revdep checks on my matrixStats package. Here is what I get:

* using log directory ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/Gviz/new/Gviz.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.36.0’
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Gviz’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    doc       4.7Mb
    extdata   2.5Mb
* 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
* 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 ... 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 examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... ERROR
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Last 50 lines of output:
  Attaching package: 'S4Vectors'

  The following objects are masked from 'package:base':

      I, expand.grid, unname

  Loading required package: IRanges
  Loading required package: GenomicRanges
  Loading required package: GenomeInfoDb
  Loading required package: grid
  > 
  > test_check("Gviz")
  Loading required package: BSgenome
  Loading required package: Biostrings
  Loading required package: XVector

  Attaching package: 'Biostrings'

  The following object is masked from 'package:grid':
      pattern

  The following object is masked from 'package:base':

      strsplit

  Loading required package: rtracklayer
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_AllClasses.R:168:5): interaction with biomart works ─────────────
  Error: Please install xml2 package
  Backtrace:
       █
    1. └─Gviz::BiomartGeneRegionTrack(...) test_AllClasses.R:168:4
    2.   └─methods::new(...)
    3.     ├─methods::initialize(value, ...)
    4.     └─Gviz::initialize(value, ...)
    5.       └─Gviz:::.local(.Object, ...)
    6.         └─Gviz:::.cacheMartData(.Object, chromosome, staged)
    7.           └─Gviz:::.fetchBMData(bmtrack, chromosome, staged)
    8.             └─biomaRt::getBM(...)
    9.               └─biomaRt:::.createHash(...)
   10.                 └─biomaRt::listEnsemblArchives()
   11.                   └─biomaRt:::.listEnsemblArchives(https = https, httr_config = list())
   12.                     ├─XML::htmlParse(content(html))
   13.                     └─httr::content(html)
   14.                       └─httr:::parse_auto(raw, type, encoding, ...)
   15.                         └─httr:::parser(...)
   16.                           └─httr:::need_package("xml2")

  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 293 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
  ‘Gviz.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR, 1 NOTE
ivanek commented 3 years ago

Hi @HenrikBengtsson, Thank you for your suggestion, I have added xml2 to suggested packages in both release and devel version. Best, Robert