Problem with updateObject #166
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lgatto
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lgatto
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* master: (24 commits) temporarily disable updateObject test - see issue #166 torture test script Fix class version problem for Spectrum1 and Spectrum2 new lines cleanup set version in initialise for Spectum only Use getClassVersion function to get class versions. Add class version to C-constructors set Spectrum class in initialize revert to previous NAnnotatedDataFrame fix new error quantifying msnexp with empty phenodata set class version in NAnnotatedDataFrame initialize fix iPQF unit test to take into account new class versions fix MSnProcess and MIAPE initialize to set class version earlier set class version in MIAPE initialize new rcpp attribs class version helper functions MSnProcess has class set in initialize and validity checks for version Initiating removal or new() class version construction inside prototype. Tix removeReporters,OnDiskMSnExp Reverting to old initialize,Spectrum (see issue #163) ... From: Laurent <lg390@cam.ac.uk> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@122190 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto
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* master: (24 commits) temporarily disable updateObject test - see issue #166 torture test script Fix class version problem for Spectrum1 and Spectrum2 new lines cleanup set version in initialise for Spectum only Use getClassVersion function to get class versions. Add class version to C-constructors set Spectrum class in initialize revert to previous NAnnotatedDataFrame fix new error quantifying msnexp with empty phenodata set class version in NAnnotatedDataFrame initialize fix iPQF unit test to take into account new class versions fix MSnProcess and MIAPE initialize to set class version earlier set class version in MIAPE initialize new rcpp attribs class version helper functions MSnProcess has class set in initialize and validity checks for version Initiating removal or new() class version construction inside prototype. Tix removeReporters,OnDiskMSnExp Reverting to old initialize,Spectrum (see issue #163) ... From: Laurent <lg390@cam.ac.uk> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@122190 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto
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Sep 7, 2017
* master: (24 commits) temporarily disable updateObject test - see issue #166 torture test script Fix class version problem for Spectrum1 and Spectrum2 new lines cleanup set version in initialise for Spectum only Use getClassVersion function to get class versions. Add class version to C-constructors set Spectrum class in initialize revert to previous NAnnotatedDataFrame fix new error quantifying msnexp with empty phenodata set class version in NAnnotatedDataFrame initialize fix iPQF unit test to take into account new class versions fix MSnProcess and MIAPE initialize to set class version earlier set class version in MIAPE initialize new rcpp attribs class version helper functions MSnProcess has class set in initialize and validity checks for version Initiating removal or new() class version construction inside prototype. Tix removeReporters,OnDiskMSnExp Reverting to old initialize,Spectrum (see issue #163) ... From: Laurent <lg390@cam.ac.uk> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@122190 bc3139a8-67e5-0310-9ffc-ced21a209358
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Hi, is this forever unfixed? I am preparing a pull request (cf #454, annotated spectrum, the current opinion of the taskforce is to add the fields to Spectrum instead of making a seprate class) that would update Spectrum. I can circumvent the vignette and unit-test issues by updating data/itraqdata.RData and inst/extdata/msx.rda manually (for now these are the two I have identified), otherwise they will not load correctly. My question relates more to the general ideas for the updating function. (Note: I personally will drop updating in http://github.com/MassBank/RMassBank for breaking changes.) |
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I had forgotten about this. I can't answer now, but this will come up soon with the new developments. |
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As described in this post to Bioc-devel, we have a problem with
updateObjectonSpectruminstances because the class version is not set in the prototype (see issue #163 for more details).This lead to
test_updateObjects.Rto fail. That failing test is now momentarily disabled until we identify a way to fix this.The text was updated successfully, but these errors were encountered: