[Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment
Aaron Lun
alun at wehi.edu.au
Thu Apr 12 18:03:37 CEST 2018
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://github.com/epurdom/clusterExperiment/issues/66>) 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://github.com/epurdom
> > /clusterExperiment/issues/66
> > <https://github.com/epurdom/clusterExperiment/issues/66>), 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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