Question

`R CMD check` failure on Linux for CoRegNet

0

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martin.grigorov ▴ 10

@6f6493f5

Last seen 7 months ago

Bulgaria

Hi,

The checks of CoRegNet fail on Linux due to missing Suggest declarations for BiocGenerics and RUnit:

* checking tests ...
  Running "runTests.R"
 ERROR
Running the tests in "tests/runTests.R" failed.
Last 13 lines of output:
  Loading required package: shiny
  Loading required package: arules
  Loading required package: Matrix

  Attaching package: "arules"

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

      abbreviate, write

  [1] TRUE
  > BiocGenerics:::testPackage("CoRegNet")
  Error in loadNamespace(x) : there is no package called "BiocGenerics"
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted

I've opened a Pull Request with a fix.

Regards,

Martin

CoRegNet • 344 views

ADD COMMENT • link updated 9 months ago by James W. MacDonald 65k • written 9 months ago by martin.grigorov ▴ 10

score 0 · Answer 1 · 2023-08-02

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 18 hours ago

United States

As with your other question, the answer is there for you to read!

Error in loadNamespace(x) : there is no package called "BiocGenerics"

Any time R says "there is no package", that's a big hint that you need to install the package that R says isn't there.

ADD COMMENT • link 9 months ago James W. MacDonald 65k

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Hi James,

Thanks again for your responses!

As I explained in my other question the dependencies should be declared in the package's DESCRIPTION file. In Bioc 3.18 a special property (_R_CHECK_SUGGESTS_ONLY_=true) is set which purpose is to break the builds/checks for all packages which were using globally installed dependencies without declaring them in their DESCRIPTION file. In devel/3.18 the package maintainers should fix the issues by explicitly listing all package's dependencies.

Regards, Martin

ADD REPLY • link 9 months ago martin.grigorov ▴ 10

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Oh, right. All questions about package development should go to the developers listserv at bioc-devel@r-project.org

ADD REPLY • link 9 months ago James W. MacDonald 65k