[Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Last night I checked in a workaround to S4Vectors. It just calls
getClass("Annotated") instead of passing the class name directly.

I'll check in a simple fix for is() today maybe to R 3.6 (devel) and
then we'll be good for now.

On Sat, Apr 14, 2018 at 8:59 AM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:

On 04/14/2018 07:21 AM, Vincent Carey wrote:

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.

I agree that renaming is not a robust solution, and would encourage Michael
to commit the change using the class definition in `is()` with more
elaborate solutions (really this is a problem with is(), where it should be
fixed, rather than introducing complicated syntax?) left for a later day.

Martin

On Sat, Apr 14, 2018 at 4:05 AM, Herv? Pag?s <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


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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
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