Re: [Bioc-devel] Submitting a new package
- Original Message - From: Charles Determan Jr deter...@umn.edu To: Bioc-devel@r-project.org Sent: Friday, March 13, 2015 11:57:24 AM Subject: [Bioc-devel] Submitting a new package I have finished a new package recently that I would like to submit to bioconductor. I have read through the package guidelines and I believe I understand the package submission process but embarrassingly I cannot figure out how to actually submit the package? Could someone kindly explain where I actually submit the package for review? See the very bottom of http://bioconductor.org/developers/package-submission/ Dan Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Submitting a new package
I have finished a new package recently that I would like to submit to bioconductor. I have read through the package guidelines and I believe I understand the package submission process but embarrassingly I cannot figure out how to actually submit the package? Could someone kindly explain where I actually submit the package for review? Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Submitting a new package
Thanks Dan, could you confirm that the email statement (packages NEAR bioconductor POINT org) means packa...@bioconductor.org ? I don't recognize the NEAR notation. Charles On Fri, Mar 13, 2015 at 1:59 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Charles Determan Jr deter...@umn.edu To: Bioc-devel@r-project.org Sent: Friday, March 13, 2015 11:57:24 AM Subject: [Bioc-devel] Submitting a new package I have finished a new package recently that I would like to submit to bioconductor. I have read through the package guidelines and I believe I understand the package submission process but embarrassingly I cannot figure out how to actually submit the package? Could someone kindly explain where I actually submit the package for review? See the very bottom of http://bioconductor.org/developers/package-submission/ Dan Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Submitting a new package
- Original Message - From: Charles Determan Jr deter...@umn.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Bioc-devel@r-project.org Sent: Friday, March 13, 2015 12:04:12 PM Subject: Re: [Bioc-devel] Submitting a new package Thanks Dan, could you confirm that the email statement ( packages NEAR bioconductor POINT org) means packa...@bioconductor.org ? I don't recognize the NEAR notation. Yes. Spammers are not supposed to recognize it either, which is why we didn't just say packa...@bioconductor.org. Dan Charles On Fri, Mar 13, 2015 at 1:59 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Charles Determan Jr deter...@umn.edu To: Bioc-devel@r-project.org Sent: Friday, March 13, 2015 11:57:24 AM Subject: [Bioc-devel] Submitting a new package I have finished a new package recently that I would like to submit to bioconductor. I have read through the package guidelines and I believe I understand the package submission process but embarrassingly I cannot figure out how to actually submit the package? Could someone kindly explain where I actually submit the package for review? See the very bottom of http://bioconductor.org/developers/package-submission/ Dan Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Dr. Charles Determan, PhD Integrated Biosciences ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Submitting a new package
Hi Dan, On 03/13/2015 12:04 PM, Dan Tenenbaum wrote: - Original Message - From: Charles Determan Jr deter...@umn.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Bioc-devel@r-project.org Sent: Friday, March 13, 2015 12:04:12 PM Subject: Re: [Bioc-devel] Submitting a new package Thanks Dan, could you confirm that the email statement ( packages NEAR bioconductor POINT org) means packa...@bioconductor.org ? I don't recognize the NEAR notation. Yes. Spammers are not supposed to recognize it either, which is why we didn't just say packa...@bioconductor.org. I think Charles means why NEAR when we normally use AT for this? Thanks, H. Dan Charles On Fri, Mar 13, 2015 at 1:59 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Charles Determan Jr deter...@umn.edu To: Bioc-devel@r-project.org Sent: Friday, March 13, 2015 11:57:24 AM Subject: [Bioc-devel] Submitting a new package I have finished a new package recently that I would like to submit to bioconductor. I have read through the package guidelines and I believe I understand the package submission process but embarrassingly I cannot figure out how to actually submit the package? Could someone kindly explain where I actually submit the package for review? See the very bottom of http://bioconductor.org/developers/package-submission/ Dan Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Dr. Charles Determan, PhD Integrated Biosciences ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] testthat instructions for website
- Original Message -
From: Michael Love michaelisaiahl...@gmail.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Friday, March 13, 2015 6:24:56 PM
Subject: Re: [Bioc-devel] testthat instructions for website
On Mar 13, 2015 9:13 PM, Dan Tenenbaum dtene...@fredhutch.org
wrote:
- Original Message -
From: Michael Love michaelisaiahl...@gmail.com
To: bioc-devel@r-project.org
Sent: Friday, March 13, 2015 6:06:39 PM
Subject: [Bioc-devel] testthat instructions for website
hi Bioc team,
Can we add some testthat instructions to the unit testing page:
http://bioconductor.org/developers/how-to/unitTesting-guidelines/
I presume the instructions would be simply to follow the basic
testthat instructions, e.g.:
https://github.com/hadley/testthat/blob/master/README.md
http://r-pkgs.had.co.nz/tests.html
...add testthat to Suggests, put tests in files starting with
'test'
inside tests/testthat/ and write a file tests/testthat.R with
specific
code in it. I think this is what the packages here are all doing:
http://bioconductor.org/help/search/index.html?q=testthat
One thing to be aware of is that if a package uses RUnit and has a
unit test fail, the detailed output of the failed test will be in
the build report. If a package uses testthat and has a test fail,
the detailed output will NOT be in the report. So the build system
needs to be tweaked to support this. Until that happens, I
hesitate to recommend that people use testthat because they won't
get to see the detailed output that they can see uf they use
RUnit.
Thanks Dan. I knew there must be something :)
Can you explain more? Isn't it just the 00check.log which gives
details in both cases?
Well, 00check.log contains the same info that is currently shown in the build
report. If an RUnit test fails, we also include the output of
tests/runTests.Rout.fail (which testthat does not produce). A not very good
example is
http://bioconductor.org/checkResults/devel/bioc-LATEST/easyRNASeq/zin2-checksrc.html
(not very good because in this case the .fail file does not really have more
info. but often it does).
Maybe we can talk offline about how to add this support. If you could give me a
toy package with a failing testthat test it would be helpful in figuring out
where the more detailed info is written (if it is).
Dan
Best,
Mike
Dan
best,
Mike
end of request, details continue below
My reasons for wanting that Bioconductor support testthat in
addition
to RUnit is that RUnit does not make it very simple to run all
tests,
which should be a very simple thing to do.
With testthat, this is simply a call to test() which lives in
devtools. With RUnit you have to do:
runTestSuite(defineTestSuite(myTest,
inst/unitTests/,test_))
Although that's not quite enough. That will not run the same test
as
Bioconductor, or as if you ran the code in the test files in your
console, because defineTestSuite picks rngKind =
Marsaglia-Multicarry and rngNormalKind = Kinderman-Ramage,
which
are not the current R default random number generators.
So then you have to do:
runTestSuite(defineTestSuite(myTest, inst/unitTests/,test_,
rngKind = default, rngNormalKind = default))
Or you could call BiocGenerics:::testPackage(), but we probably
all
agree it's better that unit testing have a documented, exported
function.
___
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https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
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https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] testthat instructions for website
- Original Message - From: Michael Love michaelisaiahl...@gmail.com To: bioc-devel@r-project.org Sent: Friday, March 13, 2015 6:06:39 PM Subject: [Bioc-devel] testthat instructions for website hi Bioc team, Can we add some testthat instructions to the unit testing page: http://bioconductor.org/developers/how-to/unitTesting-guidelines/ I presume the instructions would be simply to follow the basic testthat instructions, e.g.: https://github.com/hadley/testthat/blob/master/README.md http://r-pkgs.had.co.nz/tests.html ...add testthat to Suggests, put tests in files starting with 'test' inside tests/testthat/ and write a file tests/testthat.R with specific code in it. I think this is what the packages here are all doing: http://bioconductor.org/help/search/index.html?q=testthat One thing to be aware of is that if a package uses RUnit and has a unit test fail, the detailed output of the failed test will be in the build report. If a package uses testthat and has a test fail, the detailed output will NOT be in the report. So the build system needs to be tweaked to support this. Until that happens, I hesitate to recommend that people use testthat because they won't get to see the detailed output that they can see uf they use RUnit. Dan best, Mike end of request, details continue below My reasons for wanting that Bioconductor support testthat in addition to RUnit is that RUnit does not make it very simple to run all tests, which should be a very simple thing to do. With testthat, this is simply a call to test() which lives in devtools. With RUnit you have to do: runTestSuite(defineTestSuite(myTest, inst/unitTests/,test_)) Although that's not quite enough. That will not run the same test as Bioconductor, or as if you ran the code in the test files in your console, because defineTestSuite picks rngKind = Marsaglia-Multicarry and rngNormalKind = Kinderman-Ramage, which are not the current R default random number generators. So then you have to do: runTestSuite(defineTestSuite(myTest, inst/unitTests/,test_, rngKind = default, rngNormalKind = default)) Or you could call BiocGenerics:::testPackage(), but we probably all agree it's better that unit testing have a documented, exported function. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] testthat instructions for website
hi Bioc team, Can we add some testthat instructions to the unit testing page: http://bioconductor.org/developers/how-to/unitTesting-guidelines/ I presume the instructions would be simply to follow the basic testthat instructions, e.g.: https://github.com/hadley/testthat/blob/master/README.md http://r-pkgs.had.co.nz/tests.html ...add testthat to Suggests, put tests in files starting with 'test' inside tests/testthat/ and write a file tests/testthat.R with specific code in it. I think this is what the packages here are all doing: http://bioconductor.org/help/search/index.html?q=testthat best, Mike end of request, details continue below My reasons for wanting that Bioconductor support testthat in addition to RUnit is that RUnit does not make it very simple to run all tests, which should be a very simple thing to do. With testthat, this is simply a call to test() which lives in devtools. With RUnit you have to do: runTestSuite(defineTestSuite(myTest, inst/unitTests/,test_)) Although that's not quite enough. That will not run the same test as Bioconductor, or as if you ran the code in the test files in your console, because defineTestSuite picks rngKind = Marsaglia-Multicarry and rngNormalKind = Kinderman-Ramage, which are not the current R default random number generators. So then you have to do: runTestSuite(defineTestSuite(myTest, inst/unitTests/,test_, rngKind = default, rngNormalKind = default)) Or you could call BiocGenerics:::testPackage(), but we probably all agree it's better that unit testing have a documented, exported function. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
