[Bioc-devel] _R_CHECK_FORCE_SUGGESTS_ = false

Martin Morgan mtmorgan at fhcrc.org
Sat Sep 15 19:12:08 CEST 2012

On 09/15/2012 09:00 AM, Henrik Bengtsson wrote:
> On Sat, Sep 15, 2012 at 8:29 AM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
>> Here's another example of this:
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/PANR/moscato1-checksrc.html
>> Question to BioC core: Why not sticking with the default
> My bad: It's TRUE by default
> <quote>
> If true, give an error if suggested packages are not available.
> Default: true (but false for CRAN submission checks).
> </quote>
> (I've been using --as-cran to much lately).  Still standing by my
> comments below though.
>>   I see a suggested package as a
>> package that is not required except in rare cases.  I also sometimes

The more usual scenario is that suggested packages are used during build 
or check but not by the installed package, e.g., suggested packages used 
in vignettes or perhaps unit tests. It's hard enough to write and 
support code that works consistently across platforms, so you're a brave 
person to want to write code that also supports different package 

_R_CHECK_FORCE_SUGGESTS_=TRUE restricts the universe of available 
packages to those on cran and Bioc (mostly), which have at least a 
modicum of testing and general availability that would seem to be desirable.

Not meant to be the final word on the _R_CHECK_FORCE_SUGGESTS_ flag.


>> use them to complement each other, e.g. part of my code prefer package
>> A but if that doesn't exist it's fall back to use package B.  It's up
>> to the developer to write examples()/system tests that don't generate
>> R CMD check errors in these cases, and if they forget, then ...yes...
>> R CMD check will generate an ERROR anyway.
> /Henrik
> PS. Yue, I don't it's not possible for the package to control these
> flags/settings.
>> /Henrik
>> On Sat, Sep 15, 2012 at 7:40 AM, Yue Li <gorillayue at gmail.com> wrote:
>>> Dear list,
>>> I just submitted a new package. It builds and checks OK on the Mac and Linux servers but fails to build on the Windows server, namely 'mosacto1'. The error says:
>>> * checking package dependencies ... ERROR
>>> Package suggested but not available: 'multicore'
>>> The suggested packages are required for a complete check.
>>> Checking can be attempted without them by setting the environment
>>> variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
>>> But it seems that I can only set that environment variable _R_CHECK_FORCE_SUGGESTS_ in ~/.R/check.Renviron on my local machine not on the server. I wonder if anyone encountered the same problem when trying to submit your package before? I apologize if the issue has been addressed in some other posts that I failed to find it by Google.
>>> Thanks in advance,
>>> Yue
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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