[Bioc-devel] BiocCheck warnings and errors

[Christian Arnold]

Sorry for that, forgot to reply to all. All things clarified, thanks for
your time to address them.

On 13/09/2022 18:05, Hervé Pagès wrote:
> Let's please keep this conversation on the bioc-devel list where it
> started.
>
> On 13/09/2022 08:53, Christian Arnold wrote:
>> Hi Hervé!
>>
>> On 13/09/2022 17:47, Hervé Pagès wrote:
>>> Hi Christian,
>>>
>>> On 13/09/2022 08:03, Christian Arnold wrote:
>>>
>>>> I have a few questions regarding BiocCheck errors and warnings that I
>>>> receive for a new package version that I feel are not warranted:
>>>>
>>>>
>>>> 1. I want to use the testthat framework in combination with
>>>> devtools::test, and from my understanding, a subdirectory /testthat/
>>>> within tests has to be used for this and is created when using
>>>> devtools::test(). I still get an ERROR when using BiocCheck because I
>>>> have no .R files in tests/ but within tests/testthat:
>>>>
>>>> * Checking unit tests... * ERROR: Add a .R or .Rin file in tests/
>>>> directory or unit tests will not be run by R CMD check. See
>>>> http://bioconductor.org/developers/how-to/unitTesting-guidelines/
>>>
>>> The error message is pretty clear about **why** you must have a .R or
>>> .Rin file in tests/ It's fine that with your current setup you can run
>>> the tests with devtools::test() but that's not enough: the tests
>>> should also be run by R CMD check.
>>
>>
>> This is already clarified, thanks to another reply, I didnt have the
>> required testthat.R in the main test directory that starts the whole
>> testing and which is recognized by R CMD check as well.
>>
>>
>>>
>>>> 2. My package has many packages listed in Suggests, with a lot of
>>>> effort
>>>> I tried to move as many packages there as possible to reduce the
>>>> installation burden. From my understanding, BiocManager does NOT
>>>> install
>>>> the packages listed under /Suggests/. Thus, since I have 10+
>>>> packages in
>>>> /Suggests/ that actually enhance user functionality and may be
>>>> needed, I
>>>> wrote a helper function that automatically installs these if the user
>>>> wants, as a convenience so users dont have to install them manually on
>>>> their own. However, no I get this error:
>>>>
>>>> ERROR: Remove install() calls (found 2 times)
>>>
>>> Having BiocManager::install() calls in the package should be ok as
>>> long as those calls are **not** executed by R CMD build or R CMD
>>> check. Running R CMD build or R CMD check should never install
>>> packages on the user machine.
>>
>> They are not executed no, but the Bioc error is still raised. I guess I
>> can then just ignore it, the package is already on Bioconductor.
>>
>>>
>>>>
>>>> 3. Minor but still: Can I use Biochceck also for the devel branch?
>>>> I get
>>>> the following warning because I am checking the devel version and not
>>>> the release version:
>>>>
>>>> WARNING: y of x.y.z version should be even in release
>>>
>>> If you are going to submit your package to Bioconductor, you must
>>> check your package against BioC devel, not against the current release.
>>
>>
>> See above, I used my devel branch for BiocCheck, which has an "uneven"
>> version number as required for the devel branch but BiocCheck seems to
>> check against the "release" branch and therefore throws the warning.
>
> Yes, you're checking the devel branch of your package, I get that. But
> I suspect you're using BioC release (i.e. BioC 3.15). What I'm saying
> is that you must use BioC devel. Loading BiocManager will tell you the
> version of Bioconductor that you are using.

I see, I get you, I indeed used Bioc 3.15, that explains it. Thanks!


>
> Best,
>
> H.
>
>>
>>
>>>
>>> Hope this helps,
>>>
>>> H.
>>>
>>>
>>>>
>>>> ***Thanks for your input and thoughts!****Christian*
>>>>
>>>>     [[alternative HTML version deleted]]
>>>>
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>>>