And of course: the whole trick I described below only makes sense
if MTseeker doesn't rely on gmapR for its core functionality, that
is, if not having gmapR installed still allows the user to accomplish
something meaningful with MTseeker.
Otherwise the trick below will make MTseeker available on Windows
but Windows users won't be able to accomplish anything meaningful
with it. In that case, marking the package as unsupported on Windows
would be preferable.
Hope this makes sense,
H.
On 10/10/2018 10:26 PM, Hervé Pagès wrote:
Hi Tim,
No platform-specific dontrun capabilities AFAIK but you can use
something like:
if (requireNamespace("gmapR", quietly=TRUE)) {
...
...
}
in your man pages.
You would also need to move gmapR from Imports to Suggests.
Then make sure that MTseeker passes 'R CMD check' **without**
the gmapR package being installed. You'll need to define and set
environment variable _R_CHECK_FORCE_SUGGESTS_ to 0 for this.
Do it with:
export _R_CHECK_FORCE_SUGGESTS_=0
on Linux or Mac, or with:
set _R_CHECK_FORCE_SUGGESTS_=0
on Windows.
Once MTseeker is accepted, we'll add a .BBSoptions file with special
directive:
CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&&
This will have the effect to set the environment variable on the
Windows build machines before running 'R CMD check' there.
So MTseeker will be supported and available on all platforms.
For MTseekerData: the package doesn't seem to make any use of gmapR
so you can probably remove gmapR from its Suggests field.
Hope this helps,
H.
On 10/10/2018 07:46 AM, Tim Triche, Jr. wrote:
it looks like gmapR does not support Windows, and as a result, my
MTseeker
package cannot build on tokay1, so the Data package which requires it
also
cannot build on tokay1. Are there platform-specific dontrun
capabilities?
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_MTseekerData-5Fbuildreport-5F20181010103212.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18&s=QNKSsmQnfEAQOTI0r8dDuW_d01XzL_cL1cb5QIElLxw&e=
Short of somehow forcing gmapR to build on Windows, which I believe is
beyond my control, is there a way to declare that parts of the MTseeker
package are unsupported/unsupportable on Windows?
I suppose I could cleave off the variant-recalling portions but that
seems
a little ridiculous. The original goal was to take the non-NuMT reads
from
a given alignment, realign (only) those to rCRS/RSRS, and call against
that, for better mitochondrial haplogroup inference. We're still working
towards the full version, but even just calling variants against rCRS
with
indels is hugely useful, and the ability to screen out
haplogroup-specific
variants while retaining indels, SNVs, etc. turns out to be VERY handy.
More generally, there isn't any equivalent (AFAIK) in BioC, at all.
--t
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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