[Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/ - Bioc-devel

Sun, Oct 20, 2013 10:36 PM #

Hi Martin,

Thanks for the heads-up.  I think I've made the changes necessary, but am 
having trouble confirming whether the changes are correct on a Windows 
machine.

Could you tell me hows Bioconductor builds the Windows binaries of 
Bioconductor packages?

To see how things work, I am playing around with Biobase on svn.  I can 
build Biobase from the svn source including the pdfs of the vignettes 
using

   R CMD build Biobase

on my Windows machine.  This gives me a tar.gz file of Biobase with an 
inst/doc directory containing Rnws and pdfs of all the vignettes.  This 
shows that my LaTeX etc is working fine.

However when I run

   R CMD INSTALL --build Biobase

which is the recommended way to install a package under Windows, I get a 
zip file containing no sign of any vignette.  In fact there is no doc or 
inst or vignette directory in the zip file.

What else do I need to do to install the package from source with the 
vignettes build under Windows?

No doubt the answer is somewhere in one of the R manuals (writing R 
extensions or admin and installation perhaps) but I cannot find it.

Thanks
Gordon

PS.  I am running Rtools3.1 with:

R Under development (unstable) (2013-10-18 r64076)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils
[6] datasets  methods   base

other attached packages:
[1] Biobase_2.23.1     BiocGenerics_0.9.0

Date: Fri, 18 Oct 2013 14:58:52 -0700
From: Martin Morgan <mtmorgan at fhcrc.org>
To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Subject: [Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/

Bioconductor developers,

Thank you for your contributions to our last release, with a total of 749
packages! This is a great resource for the bioninformatics community.

No good deed goes unpunished. The 'devel' version of R no longer builds
vignettes in the inst/doc directory. Vignette sources (.Rnw or perhaps .Rmd
files) must be in the vignettes/ directory. There's a lot of work to be done to
make this happen, and we'd really like your help with this. Here's one recipe
for the neccessary changes, illustrtated with Biobase

1. Find the url of your package in the devel version of the Bioconductor svn
repository, e.g., for Biobase

   https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

2. Make a clean check-out of the source into a directory where `Biobase' does
not already exist

   svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

3. Re-name the inst/doc directory. Using svn rename preserves the commit history

   svn rename Biobase/inst/doc Biobase/vignettes

4. Increase the least significant part of the package version number in
Biobase/DESCRIPTION. I changed Biobase from 2.23.0 to 2.23.1.

5. Build the package, using the latest devel version of R

   R CMD build Biobase

6. Check that the built version contains .Rnw, .R, and .pdf files in the
inst/doc directory, e.g.,

   tar tzf Biobase_2.23.1.tar.gz |grep inst/doc

7. Make sure the built package passes R CMD check

   R CMD check Biobase_2.23.1.tar.gz

8. Review and check in your changes

   svn st Biobase
   svn diff Biobase/DESCRIPTION
   svn ci

This will work for many cases, but if you have problems please do not hesitate
to bring up issues on the mailing list.

If things go smoothly, you might wish to follow the instructions in the
BiocStyle vignette

http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle.pdf

for creating vignettes with a consistent look-and-feel. The text is wider, for
instance, so code generally formats better, and packages are easily linked to
their 'landing page' on the Bioconductor web site

Please don't hesitate to ask if there are any questions, and thanks in advance
for your continued effort to support the project.

Martin
-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}

Martin Morgan

Sun, Oct 20, 2013 11:08 PM #

On 10/20/2013 10:36 PM, Gordon K Smyth wrote:

The build machines run

     R CMD INSTALL --build Biobase_2.23.1.tar.gz

i.e., on the file created by R CMD build Biobase. This is not inconsistent with 
1.3.3 of Writing R Extensions:

"R CMD INSTALL --build pkg where pkg is either the name of a source tarball (in 
the usual .tar.gz format) or the location of the directory of the package source 
to be built. "

although there really seems to be only one way to build complete binaries. The 
Bioconductor build system reports what it's doing in the 'Summary' section 
'Command' line at

 
http://bioconductor.org/checkResults/devel/bioc-LATEST/Biobase/moscato2-buildbin.html

Martin

Thanks
Gordon

PS.  I am running Rtools3.1 with:

sessionInfo()

R Under development (unstable) (2013-10-18 r64076)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils
[6] datasets  methods   base

other attached packages:
[1] Biobase_2.23.1     BiocGenerics_0.9.0

Date: Fri, 18 Oct 2013 14:58:52 -0700
From: Martin Morgan <mtmorgan at fhcrc.org>
To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Subject: [Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/

Bioconductor developers,

Thank you for your contributions to our last release, with a total of 749
packages! This is a great resource for the bioninformatics community.

No good deed goes unpunished. The 'devel' version of R no longer builds
vignettes in the inst/doc directory. Vignette sources (.Rnw or perhaps .Rmd
files) must be in the vignettes/ directory. There's a lot of work to be done to
make this happen, and we'd really like your help with this. Here's one recipe
for the neccessary changes, illustrtated with Biobase

1. Find the url of your package in the devel version of the Bioconductor svn
repository, e.g., for Biobase

   https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

2. Make a clean check-out of the source into a directory where `Biobase' does
not already exist

   svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

3. Re-name the inst/doc directory. Using svn rename preserves the commit history

   svn rename Biobase/inst/doc Biobase/vignettes

4. Increase the least significant part of the package version number in
Biobase/DESCRIPTION. I changed Biobase from 2.23.0 to 2.23.1.

5. Build the package, using the latest devel version of R

   R CMD build Biobase

6. Check that the built version contains .Rnw, .R, and .pdf files in the
inst/doc directory, e.g.,

   tar tzf Biobase_2.23.1.tar.gz |grep inst/doc

7. Make sure the built package passes R CMD check

   R CMD check Biobase_2.23.1.tar.gz

8. Review and check in your changes

   svn st Biobase
   svn diff Biobase/DESCRIPTION
   svn ci

This will work for many cases, but if you have problems please do not hesitate
to bring up issues on the mailing list.

If things go smoothly, you might wish to follow the instructions in the
BiocStyle vignette

http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle.pdf

for creating vignettes with a consistent look-and-feel. The text is wider, for
instance, so code generally formats better, and packages are easily linked to
their 'landing page' on the Bioconductor web site

Please don't hesitate to ask if there are any questions, and thanks in advance
for your continued effort to support the project.

Martin
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

______________________________________________________________________
The information in this email is confidential and inte...{{dropped:15}}

Gordon K Smyth

Sun, Oct 20, 2013 11:37 PM #

Thanks, setting pkg to be the tar.gz file instead of the directory does 
the job.  I had not appreciated the difference.

The code on checkResults is very clear now.  I hadn't appreciated that the 
BUILD and the BUILDBIN steps were cumulative.

Thanks
Gordon

On Sun, 20 Oct 2013, Martin Morgan wrote:

On 10/20/2013 10:36 PM, Gordon K Smyth wrote:

Hi Martin,

Thanks for the heads-up.  I think I've made the changes necessary, but 
am having trouble confirming whether the changes are correct on a 
Windows machine.

Could you tell me hows Bioconductor builds the Windows binaries of 
Bioconductor packages?

To see how things work, I am playing around with Biobase on svn.  I can 
build Biobase from the svn source including the pdfs of the vignettes 
using

   R CMD build Biobase

on my Windows machine.  This gives me a tar.gz file of Biobase with an 
inst/doc directory containing Rnws and pdfs of all the vignettes. 
This shows that my LaTeX etc is working fine.

However when I run

   R CMD INSTALL --build Biobase

which is the recommended way to install a package under Windows, I get 
a zip file containing no sign of any vignette.  In fact there is no doc 
or inst or vignette directory in the zip file.

What else do I need to do to install the package from source with the 
vignettes build under Windows?

No doubt the answer is somewhere in one of the R manuals (writing R 
extensions or admin and installation perhaps) but I cannot find it.

The build machines run

   R CMD INSTALL --build Biobase_2.23.1.tar.gz

i.e., on the file created by R CMD build Biobase. This is not 
inconsistent with 1.3.3 of Writing R Extensions:

"R CMD INSTALL --build pkg where pkg is either the name of a source 
tarball (in the usual .tar.gz format) or the location of the directory 
of the package source to be built. "

although there really seems to be only one way to build complete 
binaries. The Bioconductor build system reports what it's doing in the 
'Summary' section 'Command' line at


http://bioconductor.org/checkResults/devel/bioc-LATEST/Biobase/moscato2-buildbin.html

Martin

Thanks
Gordon

PS.  I am running Rtools3.1 with:

sessionInfo()

R Under development (unstable) (2013-10-18 r64076)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils
[6] datasets  methods   base

other attached packages:
[1] Biobase_2.23.1     BiocGenerics_0.9.0

Date: Fri, 18 Oct 2013 14:58:52 -0700
From: Martin Morgan <mtmorgan at fhcrc.org>
To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Subject: [Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/

Bioconductor developers,

Thank you for your contributions to our last release, with a total of 749
packages! This is a great resource for the bioninformatics community.

No good deed goes unpunished. The 'devel' version of R no longer 
builds vignettes in the inst/doc directory. Vignette sources (.Rnw or 
perhaps .Rmd files) must be in the vignettes/ directory. There's a lot 
of work to be done to make this happen, and we'd really like your help 
with this. Here's one recipe for the neccessary changes, illustrtated 
with Biobase

1. Find the url of your package in the devel version of the 
Bioconductor svn repository, e.g., for Biobase

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

2. Make a clean check-out of the source into a directory where 
`Biobase' does not already exist

   svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

3. Re-name the inst/doc directory. Using svn rename preserves the commit 
history

   svn rename Biobase/inst/doc Biobase/vignettes

4. Increase the least significant part of the package version number in
Biobase/DESCRIPTION. I changed Biobase from 2.23.0 to 2.23.1.

5. Build the package, using the latest devel version of R

   R CMD build Biobase

6. Check that the built version contains .Rnw, .R, and .pdf files in the
inst/doc directory, e.g.,

   tar tzf Biobase_2.23.1.tar.gz |grep inst/doc

7. Make sure the built package passes R CMD check

   R CMD check Biobase_2.23.1.tar.gz

8. Review and check in your changes

   svn st Biobase
   svn diff Biobase/DESCRIPTION
   svn ci

This will work for many cases, but if you have problems please do not 
hesitate to bring up issues on the mailing list.

If things go smoothly, you might wish to follow the instructions in 
the BiocStyle vignette

http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle.pdf

for creating vignettes with a consistent look-and-feel. The text is 
wider, for instance, so code generally formats better, and packages 
are easily linked to their 'landing page' on the Bioconductor web site

Please don't hesitate to ask if there are any questions, and thanks in 
advance for your continued effort to support the project.

Martin
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}

Kasper Daniel Hansen

Mon, Oct 21, 2013 5:53 AM #

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