Re: [Bioc-devel] IRanges findOverlaps Result Different for Recent Update
If it's not documented, it should be, because Patrick did it on purpose (the output from the IntervalTree code is not sorted). We could add an argument to disable the sorting for when the extra speed is desired. But it has proven useful. On Thu, Jan 15, 2015 at 6:42 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Has it ever been documented that the return object is sorted in a specific way? I just want to make sure we think about whether that is something we want to enforce giving the possibility of using a different algorithm in the future. We could also address this by implementing (perhaps it already exists) a sort() method for the return object. That would still break existing code though. Best, Kasper On Wed, Jan 14, 2015 at 11:13 PM, Michael Lawrence lawrence.mich...@gene.com wrote: I bet there is a lot of code that depends on having the hits (conveniently) ordered by query,subject index, so we should try to restore the previous behavior. On Wed, Jan 14, 2015 at 8:00 PM, Dario Strbenac dstr7...@uni.sydney.edu.au wrote: Hello, For an identical query, the matrix results are in a different order. Consider the subject hits of the last two rows : mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.1.35 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 7 [7,] 6 6 mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.0.1 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 6 [7,] 6 7 This causes some values to be extracted in a different order by our annotationLookup function, and causes an error for the development version of Repitools on a test case which uses all.equal to compare a list to a correct list, but not for the release version which uses the release version of IRanges. Should I update the test case to have a new expected result, or is this new characteristic of findOverlaps likely to revert to the previous output soon ? The two sets of intervals to produce this result are anno and probesGR, defined in the tests.R file in the Repitools package. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] IRanges findOverlaps Result Different for Recent Update
Hi guys, Indeed, the Hits object returned by findOverlaps() is not fully sorted anymore. Now it's sorted by query hit *only* and not by query hit *and* subject hit. Fully sorting a big Hits object has a high cost, both in terms of time and memory footprint. The partial sorting is *much* cheaper: it's done using a tabulated sorting algo implemented in C that works in linear time. The partial sorting is important: it allows a very common transformation like as(hits, List) to be super fast. But the full sorting was overkill and generally not needed. Also note that the full sorting was never enforced via the validity method for Hits objects (and t(hits) was breaking that order in BioC 3.1). Now the validity method for Hits enforces the partial sorting and t(hits) preserves it. There were only 3 or 4 packages that broke in devel because of that change (typically the change broke their unit tests). I fixed them (except Repitools, but it's still on my list). The fix is easy: if having the hits fully sorted matters, just use sort() on the Hits object. The man page for ?findOverlaps will soon be updated to reflect these changes. Cheers, H. On 01/15/2015 06:42 AM, Kasper Daniel Hansen wrote: Has it ever been documented that the return object is sorted in a specific way? I just want to make sure we think about whether that is something we want to enforce giving the possibility of using a different algorithm in the future. We could also address this by implementing (perhaps it already exists) a sort() method for the return object. That would still break existing code though. Best, Kasper On Wed, Jan 14, 2015 at 11:13 PM, Michael Lawrence lawrence.mich...@gene.com wrote: I bet there is a lot of code that depends on having the hits (conveniently) ordered by query,subject index, so we should try to restore the previous behavior. On Wed, Jan 14, 2015 at 8:00 PM, Dario Strbenac dstr7...@uni.sydney.edu.au wrote: Hello, For an identical query, the matrix results are in a different order. Consider the subject hits of the last two rows : mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.1.35 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 7 [7,] 6 6 mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.0.1 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 6 [7,] 6 7 This causes some values to be extracted in a different order by our annotationLookup function, and causes an error for the development version of Repitools on a test case which uses all.equal to compare a list to a correct list, but not for the release version which uses the release version of IRanges. Should I update the test case to have a new expected result, or is this new characteristic of findOverlaps likely to revert to the previous output soon ? The two sets of intervals to produce this result are anno and probesGR, defined in the tests.R file in the Repitools package. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ 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] IRanges findOverlaps Result Different for Recent Update
My concern is mostly in user code not seen in Bioc svn. But perhaps the partial sorting (by query) is sufficient for many of those. On Thu, Jan 15, 2015 at 11:34 AM, Hervé Pagès hpa...@fredhutch.org wrote: Hi guys, Indeed, the Hits object returned by findOverlaps() is not fully sorted anymore. Now it's sorted by query hit *only* and not by query hit *and* subject hit. Fully sorting a big Hits object has a high cost, both in terms of time and memory footprint. The partial sorting is *much* cheaper: it's done using a tabulated sorting algo implemented in C that works in linear time. The partial sorting is important: it allows a very common transformation like as(hits, List) to be super fast. But the full sorting was overkill and generally not needed. Also note that the full sorting was never enforced via the validity method for Hits objects (and t(hits) was breaking that order in BioC 3.1). Now the validity method for Hits enforces the partial sorting and t(hits) preserves it. There were only 3 or 4 packages that broke in devel because of that change (typically the change broke their unit tests). I fixed them (except Repitools, but it's still on my list). The fix is easy: if having the hits fully sorted matters, just use sort() on the Hits object. The man page for ?findOverlaps will soon be updated to reflect these changes. Cheers, H. On 01/15/2015 06:42 AM, Kasper Daniel Hansen wrote: Has it ever been documented that the return object is sorted in a specific way? I just want to make sure we think about whether that is something we want to enforce giving the possibility of using a different algorithm in the future. We could also address this by implementing (perhaps it already exists) a sort() method for the return object. That would still break existing code though. Best, Kasper On Wed, Jan 14, 2015 at 11:13 PM, Michael Lawrence lawrence.mich...@gene.com wrote: I bet there is a lot of code that depends on having the hits (conveniently) ordered by query,subject index, so we should try to restore the previous behavior. On Wed, Jan 14, 2015 at 8:00 PM, Dario Strbenac dstr7...@uni.sydney.edu.au wrote: Hello, For an identical query, the matrix results are in a different order. Consider the subject hits of the last two rows : mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.1.35 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 7 [7,] 6 6 mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.0.1 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 6 [7,] 6 7 This causes some values to be extracted in a different order by our annotationLookup function, and causes an error for the development version of Repitools on a test case which uses all.equal to compare a list to a correct list, but not for the release version which uses the release version of IRanges. Should I update the test case to have a new expected result, or is this new characteristic of findOverlaps likely to revert to the previous output soon ? The two sets of intervals to produce this result are anno and probesGR, defined in the tests.R file in the Repitools package. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] IRanges findOverlaps Result Different for Recent Update
The order of results is not important for the analysis. I have updated the test case with a new expected result. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] ClassifyR Fails to Build on Windows
Hello, The development version of ClassifyR won't build on Windows. It happens for a code section in the vignette that executes a function that has a bpmapply loop. However, I'm using the default parameters by calling bpparam(), so it should work on Windows. The code in the vignette executes without problems for Linux and Mac OS. Is there a flaw in the development version of BiocParallel ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ClassifyR Fails to Build on Windows
There is no shared memory on windows so you need to make sure you require() any necessary packages on each node. Dan On January 15, 2015 5:00:22 PM PST, Dario Strbenac dstr7...@uni.sydney.edu.au wrote: Hello, The development version of ClassifyR won't build on Windows. It happens for a code section in the vignette that executes a function that has a bpmapply loop. However, I'm using the default parameters by calling bpparam(), so it should work on Windows. The code in the vignette executes without problems for Linux and Mac OS. Is there a flaw in the development version of BiocParallel ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] IRanges findOverlaps Result Different for Recent Update
Hi Michael, On 01/15/2015 11:59 AM, Michael Lawrence wrote: My concern is mostly in user code not seen in Bioc svn. I understand but the fate of that code is to get out of sync sooner or later. And sooner rather than later if it relies on undocumented behavior. But perhaps the partial sorting (by query) is sufficient for many of those. It seems to be sufficient for more than 99.5% of the packages in BioC svn :-) Note that keeping Hits objects partially sorted instead of fully sorted not only speeds up findOverlaps() but also basic operations on Hits objects like union(), t(), etc... Since we are on it, I should also mention that new in BioC 3.1 is a Hits() constructor function which takes care of partially sorting the hits, selectHits() for selecting hits in the same way the 'select' arg of findOverlaps() does, and all the comparison operations (==, =, order, sort, rank, etc..., see ?`Hits-comparison` in S4Vectors). Cheers, H. On Thu, Jan 15, 2015 at 11:34 AM, Hervé Pagès hpa...@fredhutch.org mailto:hpa...@fredhutch.org wrote: Hi guys, Indeed, the Hits object returned by findOverlaps() is not fully sorted anymore. Now it's sorted by query hit *only* and not by query hit *and* subject hit. Fully sorting a big Hits object has a high cost, both in terms of time and memory footprint. The partial sorting is *much* cheaper: it's done using a tabulated sorting algo implemented in C that works in linear time. The partial sorting is important: it allows a very common transformation like as(hits, List) to be super fast. But the full sorting was overkill and generally not needed. Also note that the full sorting was never enforced via the validity method for Hits objects (and t(hits) was breaking that order in BioC 3.1). Now the validity method for Hits enforces the partial sorting and t(hits) preserves it. There were only 3 or 4 packages that broke in devel because of that change (typically the change broke their unit tests). I fixed them (except Repitools, but it's still on my list). The fix is easy: if having the hits fully sorted matters, just use sort() on the Hits object. The man page for ?findOverlaps will soon be updated to reflect these changes. Cheers, H. On 01/15/2015 06:42 AM, Kasper Daniel Hansen wrote: Has it ever been documented that the return object is sorted in a specific way? I just want to make sure we think about whether that is something we want to enforce giving the possibility of using a different algorithm in the future. We could also address this by implementing (perhaps it already exists) a sort() method for the return object. That would still break existing code though. Best, Kasper On Wed, Jan 14, 2015 at 11:13 PM, Michael Lawrence lawrence.mich...@gene.com mailto:lawrence.mich...@gene.com wrote: I bet there is a lot of code that depends on having the hits (conveniently) ordered by query,subject index, so we should try to restore the previous behavior. On Wed, Jan 14, 2015 at 8:00 PM, Dario Strbenac dstr7...@uni.sydney.edu.au mailto:dstr7...@uni.sydney.edu.au wrote: Hello, For an identical query, the matrix results are in a different order. Consider the subject hits of the last two rows : mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.1.35 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 7 [7,] 6 6 mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.0.1 queryHits subjectHits [1,] 1 1 [2,] 1 4 [3,] 2 2 [4,] 4 1 [5,] 4 4 [6,] 6 6 [7,] 6 7 This causes some values to be extracted in a different order by our annotationLookup function, and causes an error for the development version of Repitools on a test case which uses all.equal to compare a list to a correct list, but not for the release version which uses the release
