[Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment
Michael Lawrence
lawrence.michael at gene.com
Sat Apr 14 21:25:35 CEST 2018
Last night I checked in a workaround to S4Vectors. It just calls
getClass("Annotated") instead of passing the class name directly.
I'll check in a simple fix for is() today maybe to R 3.6 (devel) and
then we'll be good for now.
On Sat, Apr 14, 2018 at 8:59 AM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:
> On 04/14/2018 07:21 AM, Vincent Carey wrote:
>>
>> But Annotated is defined in S4Vectors and RNeXML; the latter is not a
>> Bioconductor package.
>>
>> The likelihood of collisions among class names defined in different
>> packages seems pretty high
>> as S4 adoption grows. So requiring a systematic approach to
>> disambiguating
>> class references seems inevitable.
>
>
> I agree that renaming is not a robust solution, and would encourage Michael
> to commit the change using the class definition in `is()` with more
> elaborate solutions (really this is a problem with is(), where it should be
> fixed, rather than introducing complicated syntax?) left for a later day.
>
> Martin
>
>>
>>
>> On Sat, Apr 14, 2018 at 4:05 AM, Hervé Pagès <hpages at fredhutch.org> wrote:
>>
>>> How about renaming Annotated? Isn't having 2 classes around with the
>>> same name fundamentally a bad situation? No amount of workarounds will
>>> change that.
>>>
>>> H.
>>>
>>>
>>> On 04/12/2018 04:06 PM, Michael Lawrence wrote:
>>>
>>>> Yea, good idea, I was thinking of supporting :: in class names and
>>>> parsing them out. In code is better. Maybe %::%? It wouldn't have to
>>>> get a class object (for one thing, a class might not exist), because
>>>> the methods package supports a 'package' attribute on the character
>>>> vector, abstracted by packageSlot().
>>>>
>>>>
>>>>
>>>> On Thu, Apr 12, 2018 at 3:26 PM, Vincent Carey
>>>> <stvjc at channing.harvard.edu> wrote:
>>>>
>>>>> If we need to disambiguate class references, perhaps an operator
>>>>>
>>>>> could help? Along the lines of base::"::" ...
>>>>>
>>>>>
>>>>> "%c%" <- function(package,class) {
>>>>>
>>>>> pk = as.character(substitute(package))
>>>>>
>>>>> cl = as.character(substitute(class))
>>>>>
>>>>> getClass(cl, where=getNamespace(pk))
>>>>>
>>>>> }
>>>>>
>>>>>
>>>>> Biobase %c% ExpressionSet # a classRepresentation instance
>>>>>
>>>>>
>>>>> is(1:5, Biobase %c% ExpressionSet) # FALSE
>>>>>
>>>>>
>>>>> is(Biobase::ExpressionSet(), "ExpressionSet") # TRUE
>>>>>
>>>>>
>>>>> is(Biobase::ExpressionSet(), Biobase %c% ExpressionSet) # TRUE
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Apr 12, 2018 at 3:57 PM, Michael Lawrence
>>>>> <lawrence.michael at gene.com> wrote:
>>>>>
>>>>>>
>>>>>> Hi Davide,
>>>>>>
>>>>>> We can get this fixed soon, but I was hoping to hear e.g. Herve's
>>>>>> opinion first if he has one.
>>>>>>
>>>>>> Michael
>>>>>>
>>>>>> On Thu, Apr 12, 2018 at 12:53 PM, Davide Risso
>>>>>> <dar2062 at med.cornell.edu
>>>>>>>
>>>>>>>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Michael,
>>>>>>>
>>>>>>> Thanks for looking into this.
>>>>>>>
>>>>>>> Can you or someone with push permission to S4Vectors implement the
>>>>>>> workaround that you mentioned?
>>>>>>>
>>>>>>> Happy to create a pull request on Github if that helps.
>>>>>>>
>>>>>>> We’re trying to solve this to fix the clusterExperiment package build
>>>>>>> on
>>>>>>> Bioc-devel.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Davide
>>>>>>>
>>>>>>>
>>>>>>> On Apr 12, 2018, at 1:27 PM, Michael Lawrence
>>>>>>> <lawrence.michael at gene.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Yea it's basically
>>>>>>>
>>>>>>> library(S4Vectors)
>>>>>>> library(RNeXML)
>>>>>>> is(1:5, "Annotated")
>>>>>>> # Found more than one class "Annotated" in cache; using the first,
>>>>>>> from namespace 'S4Vectors'
>>>>>>> # Also defined by ‘RNeXML’
>>>>>>> # [1] FALSE
>>>>>>>
>>>>>>> But can be worked around:
>>>>>>>
>>>>>>> is(1:5, getClass("Annotated", where=getNamespace("S4Vectors"))
>>>>>>>
>>>>>>> # [1] FALSE
>>>>>>>
>>>>>>> Of course, using class objects instead of class names in every call
>>>>>>> to
>>>>>>> is() is not very palatable, but that's how it's done in all other
>>>>>>> languages, as far as I know.
>>>>>>>
>>>>>>> There is an inconsistency between new() and is() when resolving the
>>>>>>> class name. new() looks into the calling package's namespace, while
>>>>>>> is() looks at the package for the class of the 'object'. The new()
>>>>>>> approach seems sensible for that function, since packages should be
>>>>>>> abstracting the construction of their objects with constructors. The
>>>>>>> is() approach is broken though, because it's easy to imagine cases
>>>>>>> like where some foreign object is passed to a function, and the
>>>>>>> function checks the type with is().
>>>>>>>
>>>>>>> I can change is() to use the calling package as the fallback, so
>>>>>>> DataFrame(1:5) no longer produces a message. But calling it from
>>>>>>> another package, or global env, will still break, just like new().
>>>>>>> How
>>>>>>> does that sound?
>>>>>>>
>>>>>>> On the other hand, maybe we should be more careful with calls to is()
>>>>>>> and use class objects. That's a good workaround in this case, anyway,
>>>>>>> since I probably can't get the change into R before release.
>>>>>>>
>>>>>>> Michael
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Apr 12, 2018 at 9:03 AM, Aaron Lun <alun at wehi.edu.au> wrote:
>>>>>>>
>>>>>>> Well, it's not really SingleCellExperiment's problem, either.
>>>>>>>
>>>>>>> library(S4Vectors)
>>>>>>> DataFrame(1:5) # Silent, okay.
>>>>>>> library(RNeXML)
>>>>>>> DataFrame(1:5) # Prints out the message
>>>>>>> ## Found more than one class "Annotated" in cache; using the first,
>>>>>>> from namespace 'S4Vectors'
>>>>>>> ## Also defined by ‘RNeXML’
>>>>>>>
>>>>>>> Session information attached below.
>>>>>>>
>>>>>>> -Aaron
>>>>>>>
>>>>>>> sessionInfo()
>>>>>>>
>>>>>>> R Under development (unstable) (2018-03-26 r74466)
>>>>>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>>>>> Running under: Ubuntu 16.04.4 LTS
>>>>>>>
>>>>>>> Matrix products: default
>>>>>>> BLAS: /home/cri.camres.org/lun01/Software/R/trunk/lib/libRblas.so
>>>>>>> LAPACK: /home/cri.camres.org/lun01/Software/R/trunk/lib/libRlapack.so
>>>>>>>
>>>>>>> locale:
>>>>>>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>>>>>>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>>>>>>> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
>>>>>>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>>>>>
>>>>>>> attached base packages:
>>>>>>> [1] parallel stats4 stats graphics grDevices
>>>>>>> utils datasets
>>>>>>> [8] methods base
>>>>>>>
>>>>>>> other attached packages:
>>>>>>> [1] RNeXML_2.0.8 ape_5.1 S4Vectors_0.17.41
>>>>>>> [4] BiocGenerics_0.25.3
>>>>>>>
>>>>>>> loaded via a namespace (and not attached):
>>>>>>> [1] Rcpp_0.12.16 compiler_3.6.0 pillar_1.2.1
>>>>>>> [4] plyr_1.8.4 bindr_0.1.1 iterators_1.0.9
>>>>>>> [7] tools_3.6.0 uuid_0.1-2 jsonlite_1.5
>>>>>>> [10] tibble_1.4.2 nlme_3.1-137 lattice_0.20-35
>>>>>>> [13] pkgconfig_2.0.1 rlang_0.2.0 foreach_1.4.4
>>>>>>> [16] crul_0.5.2 curl_3.2 bindrcpp_0.2.2
>>>>>>> [19] httr_1.3.1 stringr_1.3.0 dplyr_0.7.4
>>>>>>> [22] xml2_1.2.0 grid_3.6.0 reshape_0.8.7
>>>>>>> [25] glue_1.2.0 data.table_1.10.4-3 R6_2.2.2
>>>>>>> [28] XML_3.98-1.10 purrr_0.2.4 reshape2_1.4.3
>>>>>>> [31] tidyr_0.8.0 magrittr_1.5 codetools_0.2-15
>>>>>>> [34] assertthat_0.2.0 bold_0.5.0 taxize_0.9.3
>>>>>>> [37] stringi_1.1.7 lazyeval_0.2.1 zoo_1.8-1
>>>>>>>
>>>>>>>
>>>>>>> On Thu, 2018-04-12 at 17:40 +0200, Elizabeth Purdom wrote:
>>>>>>>
>>>>>>> Just to follow up on my previous post. I am able to replicate the
>>>>>>> problem in the problem like in the github post from 2 years ago (http
>>>>>>> s://github.com/epurdom/clusterExperiment/issues/66
>>>>>>>
>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__
>>>>>>> github.com_epurdom_clusterExperiment_issues_66&d=DwIFaQ&c=lb
>>>>>>> 62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=27RAi9XMaRMwPy47
>>>>>>> RdOGbLATWZ3jxxsvAC3lBQmEVTo&m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6
>>>>>>> KmPXPitPvrUgI&s=PsCvulwKcgNnhI8OtnUfHYf8C9LuPyz9sGQmzKhL_rc&e=>)
>>>>>>> only now it
>>>>>>>
>>>>>>> is not the SummarizedExperiment class but the SingleCellExperiment
>>>>>>> class that has the problem. [And I was incorrect, the problem does
>>>>>>> occur in development version 2018-03-22 r74446].
>>>>>>>
>>>>>>> So this is actually a problem with the SingleCellExperiment package —
>>>>>>> sorry for the incorrect subject line.
>>>>>>>
>>>>>>> All of the best,
>>>>>>> Elizabeth
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> library(SingleCellExperiment)
>>>>>>> SingleCellExperiment()
>>>>>>>
>>>>>>> class: SingleCellExperiment
>>>>>>> dim: 0 0
>>>>>>> metadata(0):
>>>>>>> assays(0):
>>>>>>> rownames: NULL
>>>>>>> rowData names(0):
>>>>>>> colnames: NULL
>>>>>>> colData names(0):
>>>>>>> reducedDimNames(0):
>>>>>>> spikeNames(0):
>>>>>>>
>>>>>>>
>>>>>>> library(RNeXML)
>>>>>>>
>>>>>>> Loading required package: ape
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> SingleCellExperiment()
>>>>>>>
>>>>>>> Found more than one class "Annotated" in cache; using the first,
>>>>>>> from namespace 'S4Vectors'
>>>>>>> Also defined by ‘RNeXML’
>>>>>>> Found more than one class "Annotated" in cache; using the first,
>>>>>>> from namespace 'S4Vectors'
>>>>>>> Also defined by ‘RNeXML’
>>>>>>> class: SingleCellExperiment
>>>>>>> dim: 0 0
>>>>>>> metadata(0):
>>>>>>> assays(0):
>>>>>>> rownames: NULL
>>>>>>> rowData names(0):
>>>>>>> colnames: NULL
>>>>>>> colData names(0):
>>>>>>> reducedDimNames(0):
>>>>>>> spikeNames(0):
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> sessionInfo()
>>>>>>>
>>>>>>> R Under development (unstable) (2018-03-22 r74446)
>>>>>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>>>>>> Running under: OS X El Capitan 10.11.6
>>>>>>>
>>>>>>> Matrix products: default
>>>>>>> BLAS:
>>>>>>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor
>>>>>>> ks/vecLib.framework/Versions/A/libBLAS.dylib
>>>>>>> LAPACK:
>>>>>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapa
>>>>>>> ck.dylib
>>>>>>>
>>>>>>> locale:
>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>>
>>>>>>> attached base packages:
>>>>>>> [1] parallel stats4 stats graphics grDevices
>>>>>>> utils datasets methods base
>>>>>>>
>>>>>>> other attached packages:
>>>>>>> [1]
>>>>>>> RNeXML_2.0.8 ape_5.1 SingleCellE
>>>>>>> xperiment_1.1.2
>>>>>>> [4] SummarizedExperiment_1.9.16
>>>>>>> DelayedArray_0.5.30 BiocParallel_1.13.3
>>>>>>> [7]
>>>>>>> matrixStats_0.53.1 Biobase_2.39.2 GenomicRang
>>>>>>> es_1.31.23
>>>>>>> [10]
>>>>>>> GenomeInfoDb_1.15.5 IRanges_2.13.28 S4Vectors_0
>>>>>>> .17.41
>>>>>>> [13] BiocGenerics_0.25.3
>>>>>>>
>>>>>>> loaded via a namespace (and not attached):
>>>>>>> [1]
>>>>>>> Rcpp_0.12.16 pillar_1.2.1 bindr_0.1.1
>>>>>>> compiler_3.5.0
>>>>>>> [5]
>>>>>>> plyr_1.8.4 XVector_0.19.9 iterators_1.0.9
>>>>>>> bitops_1.0-6
>>>>>>> [9] tools_3.5.0 zlibbioc_1.25.0 uuid_0.1-
>>>>>>> 2 tibble_1.4.2
>>>>>>> [13] jsonlite_1.5 nlme_3.1-137 lattice_0.20-
>>>>>>> 35 pkgconfig_2.0.1
>>>>>>> [17] rlang_0.2.0 Matrix_1.2-
>>>>>>> 14 foreach_1.4.4 crul_0.5.2
>>>>>>> [21]
>>>>>>> curl_3.2 bindrcpp_0.2.2 GenomeInfoDbData_1.1.
>>>>>>> 0 dplyr_0.7.4
>>>>>>> [25]
>>>>>>> httr_1.3.1 stringr_1.3.0 xml2_1.2.0
>>>>>>> grid_3.5.0
>>>>>>> [29]
>>>>>>> glue_1.2.0 reshape_0.8.7 data.table_1.10.4-
>>>>>>> 3 R6_2.2.2
>>>>>>> [33] XML_3.98-
>>>>>>> 1.10 purrr_0.2.4 tidyr_0.8.0 reshape
>>>>>>> 2_1.4.3
>>>>>>> [37] magrittr_1.5 codetools_0.2-
>>>>>>> 15 assertthat_0.2.0 bold_0.5.0
>>>>>>> [41]
>>>>>>> taxize_0.9.3 stringi_1.1.7 lazyeval_0.2.1
>>>>>>> RCurl_1.95-4.10
>>>>>>> [45] zoo_1.8-1
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Apr 11, 2018, at 10:25 AM, Elizabeth Purdom <epurdom at stat.Berkel
>>>>>>> ey.EDU> wrote:
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> Our package clusterExperiment has suddenly started producing errors
>>>>>>> in the bioconductor devel branch because our unit tests are
>>>>>>> failing, even though we haven’t pushed any changes and they passed
>>>>>>> previously. We first noticed this on April 5th.
>>>>>>>
>>>>>>> I believe the source of these errors likely do to calls to
>>>>>>> SummarizedExperiment() creating the following messages due to
>>>>>>> conflicts in ‘RNeXML’ and ’S4Vectors’ both defining class
>>>>>>> ‘Annotated':
>>>>>>>
>>>>>>>
>>>>>>> Found more than one class "Annotated" in cache; using the first,
>>>>>>> from namespace 'S4Vectors'
>>>>>>> Also defined by ‘RNeXML’
>>>>>>>
>>>>>>> This is killing a vast number of our tests where we repeatedly use
>>>>>>> ‘expect_silent’ calls in our unit tests and SummarizedExperiment
>>>>>>> calls underlie everything.
>>>>>>>
>>>>>>> We had this message issue two years ago
>>>>>>>
>>>>>>> (https://urldefense.proofpoint.com/v2/url?u=https-3A__
>>>>>>> github.com_epurdom&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXr
>>>>>>> ryqt9KZX2qu2s&r=27RAi9XMaRMwPy47RdOGbLATWZ3jxxsvAC3lBQmEVTo&
>>>>>>> m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6KmPXPitPvrUgI&s=QasLVQB428Ql
>>>>>>> 4woG4ckrA0ljZSLRUgylm3PdN1fOn00&e=
>>>>>>> /clusterExperiment/issues/66
>>>>>>>
>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__
>>>>>>> github.com_epurdom_clusterExperiment_issues_66&d=DwIFaQ&c=lb
>>>>>>> 62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=27RAi9XMaRMwPy47
>>>>>>> RdOGbLATWZ3jxxsvAC3lBQmEVTo&m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6
>>>>>>> KmPXPitPvrUgI&s=PsCvulwKcgNnhI8OtnUfHYf8C9LuPyz9sGQmzKhL_rc&e=>),
>>>>>>> when it
>>>>>>> appeared to be a problem with two definitions of the ‘Annotated’
>>>>>>> class in two packages that are both dependencies of packages we
>>>>>>> call. At that time, Michael Lawrence posted that he would fix the
>>>>>>> problem, and it was then fixed in later versions of bioconductor/R.
>>>>>>> But it appears to be back. I am unfortunately unable to get the
>>>>>>> RNeXML package to compile from source on my computer with the
>>>>>>> current Mac OS X development binary which I just downloaded (2018-
>>>>>>> 04-05 r74542), so I haven’t been able to completely redo the code
>>>>>>> that we presented in that earlier github issue to confirm it is the
>>>>>>> exact same problem. I am having to rely on the error reports/logs
>>>>>>> from both Bioconductor and TravisCI (e.g. 2018-04-07 r74551), where
>>>>>>> this message shows up everywhere and didn’t before. Thus I’m
>>>>>>> guessing that since they are the same messages from before that the
>>>>>>> source is again the call to SummarizedExperiment.
>>>>>>>
>>>>>>> I would note that in development version 2018-03-22 r74446, where I
>>>>>>> was able to install all of the packages, I was not getting these
>>>>>>> messages.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Elizabeth Purdom
>>>>>>>
>>>>>>>
>>>>>>> [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>
>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>>>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=lb62iw4YL4RFa
>>>>>>> lcE2hQUQealT9-RXrryqt9KZX2qu2s&r=27RAi9XMaRMwPy47RdOGbLATWZ3
>>>>>>> jxxsvAC3lBQmEVTo&m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6KmPXPitPvrU
>>>>>>> gI&s=sgZkMo8EM5lXrra1obmPLWz4H4hrqm1Y2HhQRwa8IaA&e=
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt
>>>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fo
>>>>>> l6oIBKr5fVzLGchc4RvlrsYKehauLVF5_G-LWRaXM&s=UovEzK2nsWLv9tn6
>>>>>> _XmxsASzSfuAFOLSHTrOousDJOY&e=
>>>>>>
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt
>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fo
>>>> l6oIBKr5fVzLGchc4RvlrsYKehauLVF5_G-LWRaXM&s=UovEzK2nsWLv9tn6
>>>> _XmxsASzSfuAFOLSHTrOousDJOY&e=
>>>>
>>>>
>>> --
>>> 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: hpages at fredhutch.org
>>> Phone: (206) 667-5791
>>> Fax: (206) 667-1319
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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