[Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment
Vincent Carey
stvjc at channing.harvard.edu
Sat Apr 14 13:21:52 CEST 2018
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.
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
>
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