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]]
>
> _______________________________________________
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>

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