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.mich...@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 <dar2...@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.mich...@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 <a...@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@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@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=
> >
> >
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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