[Bioc-devel] annotate missing from devel

The checks seems fine but I cannot obtain it with biocLite under 2.8.0

Kasper

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite under 2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look fine for 
annotate:

  
http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html 


but not the "aquarium" builds (i.e. the builds for R-2.8/BioC-2.3):

  
http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html 


Therefore annotate will not be pushed to the BioC 2.3 public repo until 
someone
fixes its vignette.

Cheers,
H.

PS: The general page for all our builds is:

  http://bioconductor.org/checkResults/

Kasper

Hi Herve,

Herve Pages wrote:

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite under 2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look fine for 
annotate:

  
http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html 


but not the "aquarium" builds (i.e. the builds for R-2.8/BioC-2.3):

  
http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html 


Therefore annotate will not be pushed to the BioC 2.3 public repo 
until someone
fixes its vignette.

Unfortunately that vignette is unfixable - it is based on the old 
Homologene/env packages, so will need to be almost completely rewritten 
to use the new InParanoid/SQLite packages.

I should be able to replace it with something reasonable either this 
week or the next. In the meantime I will just rename it so it won't 
interfere with the build.

Best,

Jim

Cheers,
H.

PS: The general page for all our builds is:

  http://bioconductor.org/checkResults/

Kasper

Hi Herve,

Herve Pages wrote:

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite under 2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look fine 
for annotate:

  
http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html 


but not the "aquarium" builds (i.e. the builds for R-2.8/BioC-2.3):

  
http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html 


Therefore annotate will not be pushed to the BioC 2.3 public repo 
until someone
fixes its vignette.

Unfortunately that vignette is unfixable - it is based on the old 
Homologene/env packages, so will need to be almost completely 
rewritten to use the new InParanoid/SQLite packages.

I should be able to replace it with something reasonable either this 
week or the next. In the meantime I will just rename it so it won't 
interfere with the build.

Best,

Jim

Cheers,
H.

PS: The general page for all our builds is:

  http://bioconductor.org/checkResults/

Kasper

Hi all,

Will there be an ETA on a fix for this problem? There seems to be many
packages that I cannot load because they depend on annotate.

On Wed, May 7, 2008 at 10:56 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:

Hi Jim,

I was planning to write a short vignette to replace the broken hsahomology
one (since we have previously deprecated that).  I was going to replace it
with one that demonstrates how you can use the newer inparanoid packages.  I
just have not had time to do it yet.  Please let me know if you have this
tackled already, but if not it is already on my "to do " list.  In the
meantime, dropping the broken vignette that describes a defunct package
seems like a step in the right direction.


  Marc





James W. MacDonald wrote:

Hi Herve,

Herve Pages wrote:

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite under
2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look fine for
annotate:


http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html

but not the "aquarium" builds (i.e. the builds for R-2.8/BioC-2.3):


http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html

Therefore annotate will not be pushed to the BioC 2.3 public repo
until someone
fixes its vignette.

Unfortunately that vignette is unfixable - it is based on the old
Homologene/env packages, so will need to be almost completely rewritten to
use the new InParanoid/SQLite packages.

I should be able to replace it with something reasonable either this
week or the next. In the meantime I will just rename it so it won't
interfere with the build.

Best,

Jim

Cheers,
H.

PS: The general page for all our builds is:

 http://bioconductor.org/checkResults/

Kasper

       [[alternative HTML version deleted]]

Hi Sean,

I know...I have all bioconductor source files checked out. There are some
folks here who want to use some of my packages that depend on packages which
depend on annotate. For the short term, it is fine to install manually with
the vignette being somewhat broken. I just wanted to make my life a little
easier and tell them to grab it via biocLite rather than having them install
svn, etc. It has been about a week since others brought it up, and I just
wanted to know about an ETA so I can tell them.

On Wed, May 14, 2008 at 1:39 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:

On Wed, May 14, 2008 at 8:00 AM, Tony Chiang <tchiang at fhcrc.org> wrote:

Hi all,

Will there be an ETA on a fix for this problem? There seems to be many
packages that I cannot load because they depend on annotate.

Tony,

The package appears to install just fine for me doing (from the
command line--your mileage may vary):

svn export
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
R CMD INSTALL annotate

This is on a unix-like system (Mac) and of course requires an svn
client and build tools for your system but, once installed, it will
allow installation of those other packages.

Hope that helps in the short term.

Sean

On Wed, May 7, 2008 at 10:56 PM, Marc Carlson <mcarlson at fhcrc.org>

wrote:

Hi Jim,

I was planning to write a short vignette to replace the broken

hsahomology

one (since we have previously deprecated that).  I was going to replace

it

with one that demonstrates how you can use the newer inparanoid

packages.  I

just have not had time to do it yet.  Please let me know if you have

this

tackled already, but if not it is already on my "to do " list.  In the
meantime, dropping the broken vignette that describes a defunct package
seems like a step in the right direction.


  Marc





James W. MacDonald wrote:

Hi Herve,

Herve Pages wrote:

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite under
2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look fine

for

annotate:

http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html

but not the "aquarium" builds (i.e. the builds for R-2.8/BioC-2.3):

http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html

Therefore annotate will not be pushed to the BioC 2.3 public repo
until someone
fixes its vignette.

Unfortunately that vignette is unfixable - it is based on the old
Homologene/env packages, so will need to be almost completely

rewritten to

use the new InParanoid/SQLite packages.

I should be able to replace it with something reasonable either this
week or the next. In the meantime I will just rename it so it won't
interfere with the build.

Best,

Jim

Cheers,
H.

PS: The general page for all our builds is:

 http://bioconductor.org/checkResults/

Kasper

       [[alternative HTML version deleted]]

       [[alternative HTML version deleted]]

I definitely agree with you; but as it is not my package I don't think the
maintainers would appreciate me fiddling with it. Herve told us that the
Vignette was broken, and both Jim and Marc said they would update it within
a week or so. I guess my e-mail was just a gentle reminder (I know Jim and
Marc are both busy). Until the vignette is fixed and the changes committed
to svn, biocLite won't work.

Tony

On Wed, May 14, 2008 at 2:16 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:

On Wed, May 14, 2008 at 9:05 AM, Tony Chiang <tchiang at fhcrc.org> wrote:

Hi Sean,

I know...I have all bioconductor source files checked out. There are some
folks here who want to use some of my packages that depend on packages

which

depend on annotate. For the short term, it is fine to install manually

with

the vignette being somewhat broken. I just wanted to make my life a

little

easier and tell them to grab it via biocLite rather than having them

install

svn, etc. It has been about a week since others brought it up, and I just
wanted to know about an ETA so I can tell them.

If the only issue is the vignette, then the best bet might be to
remove that particular vignette for now and replace it when it is
complete?

Sean

On Wed, May 14, 2008 at 1:39 PM, Sean Davis <sdavis2 at mail.nih.gov>

wrote:

On Wed, May 14, 2008 at 8:00 AM, Tony Chiang <tchiang at fhcrc.org> wrote:

Hi all,

Will there be an ETA on a fix for this problem? There seems to be many
packages that I cannot load because they depend on annotate.

Tony,

The package appears to install just fine for me doing (from the
command line--your mileage may vary):

svn export
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
R CMD INSTALL annotate

This is on a unix-like system (Mac) and of course requires an svn
client and build tools for your system but, once installed, it will
allow installation of those other packages.

Hope that helps in the short term.

Sean

On Wed, May 7, 2008 at 10:56 PM, Marc Carlson <mcarlson at fhcrc.org>

wrote:

Hi Jim,

I was planning to write a short vignette to replace the broken

hsahomology

one (since we have previously deprecated that).  I was going to

replace

it

with one that demonstrates how you can use the newer inparanoid

packages.  I

just have not had time to do it yet.  Please let me know if you have

this

tackled already, but if not it is already on my "to do " list.  In

the

meantime, dropping the broken vignette that describes a defunct

package

seems like a step in the right direction.


  Marc





James W. MacDonald wrote:

Hi Herve,

Herve Pages wrote:

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite

under

2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look

fine

for

annotate:

http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html

but not the "aquarium" builds (i.e. the builds for

R-2.8/BioC-2.3):

http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html

Therefore annotate will not be pushed to the BioC 2.3 public repo
until someone
fixes its vignette.

Unfortunately that vignette is unfixable - it is based on the old
Homologene/env packages, so will need to be almost completely

rewritten to

use the new InParanoid/SQLite packages.

I should be able to replace it with something reasonable either

this

week or the next. In the meantime I will just rename it so it won't
interfere with the build.

Best,

Jim

Cheers,
H.

PS: The general page for all our builds is:

 http://bioconductor.org/checkResults/

Kasper

       [[alternative HTML version deleted]]

       [[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

My bad. Marc is going to fix the vignette, and in the meantime I stuck 
an extension on the old vignette so it would be ignored in the build 
process. However, I didn't change the depends field to remove 
hsahomology and xlahomology.

Fixed now.

Best,

Jim



Tony Chiang wrote:

I definitely agree with you; but as it is not my package I don't 
think the
maintainers would appreciate me fiddling with it. Herve told us that the
Vignette was broken, and both Jim and Marc said they would update it 
within
a week or so. I guess my e-mail was just a gentle reminder (I know 
Jim and
Marc are both busy). Until the vignette is fixed and the changes 
committed
to svn, biocLite won't work.

Tony

On Wed, May 14, 2008 at 2:16 PM, Sean Davis <sdavis2 at mail.nih.gov> 
wrote:

On Wed, May 14, 2008 at 9:05 AM, Tony Chiang <tchiang at fhcrc.org> wrote:

Hi Sean,

I know...I have all bioconductor source files checked out. There 
are some
folks here who want to use some of my packages that depend on packages

which

depend on annotate. For the short term, it is fine to install manually

with

the vignette being somewhat broken. I just wanted to make my life a

little

easier and tell them to grab it via biocLite rather than having them

install

svn, etc. It has been about a week since others brought it up, and 
I just
wanted to know about an ETA so I can tell them.

If the only issue is the vignette, then the best bet might be to
remove that particular vignette for now and replace it when it is
complete?

Sean

On Wed, May 14, 2008 at 1:39 PM, Sean Davis <sdavis2 at mail.nih.gov>

wrote:

On Wed, May 14, 2008 at 8:00 AM, Tony Chiang <tchiang at fhcrc.org> 
wrote:

Hi all,

Will there be an ETA on a fix for this problem? There seems to be 
many
packages that I cannot load because they depend on annotate.

Tony,

The package appears to install just fine for me doing (from the
command line--your mileage may vary):

svn export
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
R CMD INSTALL annotate

This is on a unix-like system (Mac) and of course requires an svn
client and build tools for your system but, once installed, it will
allow installation of those other packages.

Hope that helps in the short term.

Sean

On Wed, May 7, 2008 at 10:56 PM, Marc Carlson <mcarlson at fhcrc.org>

wrote:

Hi Jim,

I was planning to write a short vignette to replace the broken

hsahomology

one (since we have previously deprecated that).  I was going to

replace

it

with one that demonstrates how you can use the newer inparanoid

packages.  I

just have not had time to do it yet.  Please let me know if you 
have

this

tackled already, but if not it is already on my "to do " list.  In

the

meantime, dropping the broken vignette that describes a defunct

package

seems like a step in the right direction.


  Marc





James W. MacDonald wrote:

Hi Herve,

Herve Pages wrote:

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite

under

2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look

fine

for

annotate:

http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html 

but not the "aquarium" builds (i.e. the builds for

R-2.8/BioC-2.3):

http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html 

Therefore annotate will not be pushed to the BioC 2.3 public repo
until someone
fixes its vignette.

Unfortunately that vignette is unfixable - it is based on the old
Homologene/env packages, so will need to be almost completely

rewritten to

use the new InParanoid/SQLite packages.

I should be able to replace it with something reasonable either

this

week or the next. In the meantime I will just rename it so it 
won't
interfere with the build.

Best,

Jim

Cheers,
H.

PS: The general page for all our builds is:

 http://bioconductor.org/checkResults/

Kasper

       [[alternative HTML version deleted]]

       [[alternative HTML version deleted]]

    [[alternative HTML version deleted]]

I have replaced the useHomology vignette with a newer one that describes 
the newer inparanoid based packages.

   Marc


James W. MacDonald wrote:

My bad. Marc is going to fix the vignette, and in the meantime I stuck 
an extension on the old vignette so it would be ignored in the build 
process. However, I didn't change the depends field to remove 
hsahomology and xlahomology.

Fixed now.

Best,

Jim



Tony Chiang wrote:

I definitely agree with you; but as it is not my package I don't 
think the
maintainers would appreciate me fiddling with it. Herve told us that the
Vignette was broken, and both Jim and Marc said they would update it 
within
a week or so. I guess my e-mail was just a gentle reminder (I know 
Jim and
Marc are both busy). Until the vignette is fixed and the changes 
committed
to svn, biocLite won't work.

Tony

On Wed, May 14, 2008 at 2:16 PM, Sean Davis <sdavis2 at mail.nih.gov> 
wrote:

On Wed, May 14, 2008 at 9:05 AM, Tony Chiang <tchiang at fhcrc.org> wrote:

Hi Sean,

I know...I have all bioconductor source files checked out. There 
are some
folks here who want to use some of my packages that depend on packages

which

depend on annotate. For the short term, it is fine to install manually

with

the vignette being somewhat broken. I just wanted to make my life a

little

easier and tell them to grab it via biocLite rather than having them

install

svn, etc. It has been about a week since others brought it up, and 
I just
wanted to know about an ETA so I can tell them.

If the only issue is the vignette, then the best bet might be to
remove that particular vignette for now and replace it when it is
complete?

Sean

On Wed, May 14, 2008 at 1:39 PM, Sean Davis <sdavis2 at mail.nih.gov>

wrote:

On Wed, May 14, 2008 at 8:00 AM, Tony Chiang <tchiang at fhcrc.org> 
wrote:

Hi all,

Will there be an ETA on a fix for this problem? There seems to be 
many
packages that I cannot load because they depend on annotate.

Tony,

The package appears to install just fine for me doing (from the
command line--your mileage may vary):

svn export
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
R CMD INSTALL annotate

This is on a unix-like system (Mac) and of course requires an svn
client and build tools for your system but, once installed, it will
allow installation of those other packages.

Hope that helps in the short term.

Sean

On Wed, May 7, 2008 at 10:56 PM, Marc Carlson <mcarlson at fhcrc.org>

wrote:

Hi Jim,

I was planning to write a short vignette to replace the broken

hsahomology

one (since we have previously deprecated that).  I was going to

replace

it

with one that demonstrates how you can use the newer inparanoid

packages.  I

just have not had time to do it yet.  Please let me know if you 
have

this

tackled already, but if not it is already on my "to do " list.  In

the

meantime, dropping the broken vignette that describes a defunct

package

seems like a step in the right direction.


  Marc





James W. MacDonald wrote:

Hi Herve,

Herve Pages wrote:

Hi Kasper,

Kasper Daniel Hansen wrote:

The checks seems fine but I cannot obtain it with biocLite

under

2.8.0

The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look

fine

for

annotate:

http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html 

but not the "aquarium" builds (i.e. the builds for

R-2.8/BioC-2.3):

http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html 

Therefore annotate will not be pushed to the BioC 2.3 public repo
until someone
fixes its vignette.

Unfortunately that vignette is unfixable - it is based on the old
Homologene/env packages, so will need to be almost completely

rewritten to

use the new InParanoid/SQLite packages.

I should be able to replace it with something reasonable either

this

week or the next. In the meantime I will just rename it so it 
won't
interfere with the build.

Best,

Jim

Cheers,
H.

PS: The general page for all our builds is:

 http://bioconductor.org/checkResults/

Kasper

       [[alternative HTML version deleted]]

       [[alternative HTML version deleted]]

    [[alternative HTML version deleted]]