[Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment
Michael Lawrence
lawrence.michael at gene.com
Fri Apr 13 01:06:21 CEST 2018
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=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=27RAi9XMaRMwPy47RdOGbLATWZ3jxxsvAC3lBQmEVTo&m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6KmPXPitPvrUgI&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-RXrryqt9KZX2qu2s&r=27RAi9XMaRMwPy47RdOGbLATWZ3jxxsvAC3lBQmEVTo&m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6KmPXPitPvrUgI&s=QasLVQB428Ql4woG4ckrA0ljZSLRUgylm3PdN1fOn00&e=
>> > /clusterExperiment/issues/66
>> >
>> > <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_epurdom_clusterExperiment_issues_66&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=27RAi9XMaRMwPy47RdOGbLATWZ3jxxsvAC3lBQmEVTo&m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6KmPXPitPvrUgI&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.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=27RAi9XMaRMwPy47RdOGbLATWZ3jxxsvAC3lBQmEVTo&m=FD3EbY8tWuTuwKQOAOgm-DLN6S1TI6KmPXPitPvrUgI&s=sgZkMo8EM5lXrra1obmPLWz4H4hrqm1Y2HhQRwa8IaA&e=
>> >
>> >
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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