[Bioc-devel] Package "not supported" on some platforms, and dependent packages

----- Original Message -----

From: "Kevin RUE" <kevinrue67 at gmail.com>
To: "bioc-devel" <bioc-devel at r-project.org>
Sent: Tuesday, October 18, 2016 3:28:23 PM
Subject: [Bioc-devel] Package "not supported" on some platforms,

and dependent packages

Hi all,

Heartless logic works as follows:

  - ensemblVEP is "not supported" on Windows (build report
  <http://bioconductor.org/checkResults/devel/bioc-LATEST/ensemblVEP/>).
  Completely understandable.
  - My package depends on ensemblVEP.
  - The build system reports an error on Windows for my package
because "dependency
  'ensemblVEP' is not available for package 'TVTB'" (build report
  <http://bioconductor.org/checkResults/devel/bioc-

LATEST/TVTB/tokay2-buildsrc.html>

  )
  - As a result, the landing page for my package reports "build error" (
  page <https://www.bioconductor.org/packages/release/bioc/html/

TVTB.html>)

I was hoping to benefit of the same treatment as the ensemblVEP package,
that is, skipping the nightly build on the Windows machine, to get the

nice

green light "build OK" on the landing page.

I suppose this is something to control in the build system, right? Or do

I

have to put any kind of keyword in one of my package files?
Thanks!

The build system is heartless. ;)
ensemblVEP is marked as unsupported on Windows by virtue of a .BBSoptions
file in the top level (at the same level as DESCRIPTION) containing one
line:

UnsupportedPlatforms: win

If you add that to your package it will stop building (and failing) on
windows.

If ensemblVEP is ever again supported on windows (I don't know if this is
planned) you'll need to remove that file.

Dan

All the best,
Kevin

      [[alternative HTML version deleted]]

Arrrrgh, I could have looked better in the Git mirror code ;)

Anyway, thanks a lot for the tip!

No worries about removing the file if the parent package gets supported.
However, I've never tried to run the VEP script on Windows, which I expect
is pre-requisite for the package building successfully there. Might not be
that easy. Anyway, future will tell, and I'll keep an eye out for it!

Cheers
Kevin


On Tue, Oct 18, 2016 at 11:44 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

----- Original Message -----

From: "Kevin RUE" <kevinrue67 at gmail.com>
To: "bioc-devel" <bioc-devel at r-project.org>
Sent: Tuesday, October 18, 2016 3:28:23 PM
Subject: [Bioc-devel] Package "not supported" on some platforms,

and dependent packages

Hi all,

Heartless logic works as follows:

  - ensemblVEP is "not supported" on Windows (build report
  <http://bioconductor.org/checkResults/devel/bioc-LATEST/ensemblVEP/>).
  Completely understandable.
  - My package depends on ensemblVEP.
  - The build system reports an error on Windows for my package
because "dependency
  'ensemblVEP' is not available for package 'TVTB'" (build report
  <http://bioconductor.org/checkResults/devel/bioc-

LATEST/TVTB/tokay2-buildsrc.html>

  )
  - As a result, the landing page for my package reports "build error" (
  page <https://www.bioconductor.org/packages/release/bioc/html/

TVTB.html>)

I was hoping to benefit of the same treatment as the ensemblVEP package,
that is, skipping the nightly build on the Windows machine, to get the

nice

green light "build OK" on the landing page.

I suppose this is something to control in the build system, right? Or do

I

have to put any kind of keyword in one of my package files?
Thanks!

The build system is heartless. ;)
ensemblVEP is marked as unsupported on Windows by virtue of a .BBSoptions
file in the top level (at the same level as DESCRIPTION) containing one
line:

UnsupportedPlatforms: win

If you add that to your package it will stop building (and failing) on
windows.

If ensemblVEP is ever again supported on windows (I don't know if this is
planned) you'll need to remove that file.

Dan

All the best,
Kevin

      [[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

Just fyi, as stated in the NEWS, ensemblVEP >= 1.12.0 is not supported
on windows because the Ensembl VEP tool >= 84 requires tabix.

Valerie


On 10/18/2016 04:01 PM, Kevin RUE wrote:

Arrrrgh, I could have looked better in the Git mirror code ;)

Anyway, thanks a lot for the tip!

No worries about removing the file if the parent package gets supported.
However, I've never tried to run the VEP script on Windows, which I

expect

is pre-requisite for the package building successfully there. Might not

be

that easy. Anyway, future will tell, and I'll keep an eye out for it!

Cheers
Kevin


On Tue, Oct 18, 2016 at 11:44 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

----- Original Message -----

From: "Kevin RUE" <kevinrue67 at gmail.com>
To: "bioc-devel" <bioc-devel at r-project.org>
Sent: Tuesday, October 18, 2016 3:28:23 PM
Subject: [Bioc-devel] Package "not supported" on some platforms,

and dependent packages

Hi all,

Heartless logic works as follows:

  - ensemblVEP is "not supported" on Windows (build report
  <http://bioconductor.org/checkResults/devel/bioc-LATEST/ensemblVEP/

).

  Completely understandable.
  - My package depends on ensemblVEP.
  - The build system reports an error on Windows for my package
because "dependency
  'ensemblVEP' is not available for package 'TVTB'" (build report
  <http://bioconductor.org/checkResults/devel/bioc-

LATEST/TVTB/tokay2-buildsrc.html>

  )
  - As a result, the landing page for my package reports "build error"

(

  page <https://www.bioconductor.org/packages/release/bioc/html/

TVTB.html>)

I was hoping to benefit of the same treatment as the ensemblVEP

package,

that is, skipping the nightly build on the Windows machine, to get the

nice

green light "build OK" on the landing page.

I suppose this is something to control in the build system, right? Or

do

I

have to put any kind of keyword in one of my package files?
Thanks!

The build system is heartless. ;)
ensemblVEP is marked as unsupported on Windows by virtue of a

.BBSoptions

file in the top level (at the same level as DESCRIPTION) containing one
line:

UnsupportedPlatforms: win

If you add that to your package it will stop building (and failing) on
windows.

If ensemblVEP is ever again supported on windows (I don't know if this

is

planned) you'll need to remove that file.

Dan

All the best,
Kevin

      [[alternative HTML version deleted]]

      [[alternative HTML version deleted]]

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