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

[Michael Lawrence]

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
 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
>  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 
>> 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
>> > 
>> > 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  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-8LC_COLLATE=en_GB.UTF-8
>> > [5] LC_MONETARY=en_GB.UTF-8LC_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  stats4stats graphics  grDevices
>> > utils datasets
>> > [8] methods   base
>> >
>> > other attached packages:
>> > [1] RNeXML_2.0.8ape_5.1 S4Vectors_0.17.41
>> > [4] BiocGenerics_0.25.3
>> >
>> > loaded via a namespace (and not attached):
>> > [1] Rcpp_0.12.16compiler_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  

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

[Vincent Carey]

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  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 
> 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  >
> > 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  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-8LC_COLLATE=en_GB.UTF-8
> > [5] LC_MONETARY=en_GB.UTF-8LC_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  stats4stats graphics  grDevices
> > utils datasets
> > [8] methods   base
> >
> > other attached packages:
> > [1] RNeXML_2.0.8ape_5.1 S4Vectors_0.17.41
> > [4] BiocGenerics_0.25.3
> >
> > loaded via a namespace (and not attached):
> > [1] Rcpp_0.12.16compiler_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_1.4.2nlme_3.1-137lattice_0.20-35
> > [13] pkgconfig_2.0.1 rlang_0.2.0 foreach_1.4.4
> > [16] crul_0.5.2  curl_3.2bindrcpp_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_1.5codetools_0.2-15
> > [34] 

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

[Michael Lawrence]

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  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 
> 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  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-8LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8LC_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  stats4stats graphics  grDevices
> utils datasets
> [8] methods   base
>
> other attached packages:
> [1] RNeXML_2.0.8ape_5.1 S4Vectors_0.17.41
> [4] BiocGenerics_0.25.3
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.16compiler_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_1.4.2nlme_3.1-137lattice_0.20-35
> [13] pkgconfig_2.0.1 rlang_0.2.0 foreach_1.4.4
> [16] crul_0.5.2  curl_3.2bindrcpp_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_1.5codetools_0.2-15
> [34] assertthat_0.2.0bold_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
> )
> 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 

Re: [Bioc-devel] Suggested edits to support site posting guide

[Leonardo Collado Torres]

Hi Mike,

I just added a few comments to your google doc. Thanks for doing this!

Best,
Leo

On Thu, Apr 12, 2018 at 11:23 AM, Michael Love
 wrote:
>
>
> dear all,
>
> I've edited the text from the posting guide
>  to update it a
> bit.
>
> For example, some of the text still referred to the mailing list
> :
> "Compose a new message with a new subject line".
>
> Mostly, though, I wanted to emphasize posting all of their R code and
> information about the experiment, which is often missing from support site
> posts. The self-contained example with data and code is rarely possible
> because many Bioc users have large datasets that can't be shared.
>
> Curious if this is useful or if others have suggestions. The following
> link allows edits:
>
> https://docs.google.com/document/d/1baiBUYB8E02KMbaojjoo-
> tKV3Ctd9sA5lVCvwFIWquA/edit?usp=sharing
>
> best,
> Mike
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

[Michael Lawrence]

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  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-8LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8LC_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  stats4stats graphics  grDevices
> utils datasets
> [8] methods   base
>
> other attached packages:
> [1] RNeXML_2.0.8ape_5.1 S4Vectors_0.17.41
> [4] BiocGenerics_0.25.3
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.16compiler_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_1.4.2nlme_3.1-137lattice_0.20-35
> [13] pkgconfig_2.0.1 rlang_0.2.0 foreach_1.4.4
> [16] crul_0.5.2  curl_3.2bindrcpp_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_1.5codetools_0.2-15
> [34] assertthat_0.2.0bold_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
>> ) 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):

Re: [Bioc-devel] Setup for pushing changes in unifiedWMWqPCR to bioconductor git.

[Obenchain, Valerie]

Hi,

On 04/12/2018 03:02 AM, Joris Meys wrote:

Hi all,

For the package unifiedWMWqPCR I want to push some updates on the
documentation, but apparently I don't have access to the bioconductor git
any longer. I had to completely reinstall my system here, so probably
either my key got lost, or I'm using the wrong account to push.

I tried to find out what key and user was registered, but couldn't find it.
Hence a few questions:

- Is there any way to find out how I am registered today (i.e. name and
public key)?

For now this is still a manual process. Soon we hope to have an app that you 
can interact with that will supply this information.

As user 'j.meyes' you have access to unifiedWMWqPCR and we have 3 keys for you:

~/git.bioconductor.org/admin/gitolite-admin/keydir >cat key-1/j.meys.pub
ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCoPGY+EOzCkrmxQ6CJS9r4PHpwoSJTxdFUzZ2jiS3dV5uJonYdAQKj/q7Sm0y154xUk8aUfIaJgOYTkLGTm8RF9xKpC5O3bKJe3QR4NnTd2+VesnDv3dmVpidAd42ufOp2c/F4pG0xbU7uxq8LVR1PLZMGJH0KqywQ9BJ+NKCyQmRc1BwcC+q3mHOKiprewhlkLwwy416ZVUB/MPciKTciaHV7IoTT/yDlyxq2I+68IiTt+i+WlGfG3uYwi4sdry+FpK0YR7AzZY4+l+KJBA3+YRx+6M9yJF1xt/BDLo84z7NAu6KVElAP98GuxheKT0VRu5YtfdPBLmLEnG37plwx

~/git.bioconductor.org/admin/gitolite-admin/keydir >cat key-2/j.meys.pub
ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDOT4AHsEmXzNPptDOOWSBMBhpE3Tebe5rnW4Vo9IH7OME4cxBCZwufZFGRDwE27SjLXJWYDObo4KuLcqmoC0iEzRE03JR9Eq/0EPnit4K6wrkUUjNsN1jVhWhjsx755qI0mc9NigokyoTa2wqXwWN2ADDgAqM0BaTjdoI8MYU3ckEgfOKrNBEYOu4yuXl5+sSCSPVKuAMR996F30s4iJcajBMhb9lppfRvthvbUf70w9osGCUsZz4lLwXFuG4h45ve5D+FiJb0aVehkxDJIl0FTLoY65Mm4vYCtpHR1SZGibg7xGLMYgz1ioQf3Wa2JElO70lrpCd6Zczn1Baa4Aqn


~/git.bioconductor.org/admin/gitolite-admin/keydir >cat key-3/j.meys.pub
ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCd6VZDI5I2ared2rEUQZOCI8xtlsn7EEKbcrASMz60ug8bAXD73NpIOyPDonpyjluGjb+0/xy/j7OTI+yx5CMFdVc9mUVZMHS9z0iTYHygnXCNmTXgMLwMDW7u2h8D98DmrHzE5uhdxLDIWE/1Cq42eckcgFexQLt4GkB98NZFpXYqIJzJWedWOy3PCfBGrXYC6V4L+sJyRzGq8xUJ/KMVRBwPMgQQC4tUjfxtgWjCtpe+H9JFCNHkBOpwDRLYAdsuxaOPuKDAhUN/GV9wHUUihbz5iq8SS3Rt1MFtkwQ7u8lu4kpUHMTregCQuhkgkv9MuROZahfXeMGXtE6VsHEx




- I'm JoFAM on github, but the repo is in an organization called
CenterForStatistics-UGent. What github name do I use then for sending a new
public key?

Do you not have access to these 3 keys? I would try those first.

If you have lost all 3 keys, you can register as user 'j.meyes' and give your 
github username 'JoFAM' instead of a key. We will scrape
https://github.com/JoFAM.keys for keys (if they differ from the 3 above).



- I use my work email for maintaining the package, but my account is set to
my personal email. Is that a problem and if so, how should I tackle that?

I'm not sure what you mean by 'account'. Ideally you register in the Google 
Sheet with the same email that is in DESCRIPTION in your package.

Valerie




Thank you in advance.





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

[Aaron Lun]

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-8LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8LC_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  stats4stats graphics  grDevices
utils datasets 
[8] methods   base 

other attached packages:
[1] RNeXML_2.0.8ape_5.1 S4Vectors_0.17.41  
[4] BiocGenerics_0.25.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16compiler_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_1.4.2nlme_3.1-137lattice_0.20-35
[13] pkgconfig_2.0.1 rlang_0.2.0 foreach_1.4.4  
[16] crul_0.5.2  curl_3.2bindrcpp_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_1.5codetools_0.2-15   
[34] assertthat_0.2.0bold_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
> ) 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  stats4stats graphics  grDevices
> > utils datasets  methods   base 
> > 
> > other attached packages:
> >  [1]
> > RNeXML_2.0.8ape_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 

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

[Elizabeth Purdom]

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 
(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/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.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  stats4stats graphics  grDevices utils datasets  
> methods   base 
> 
> other attached packages:
>  [1] RNeXML_2.0.8ape_5.1 
> SingleCellExperiment_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  
> GenomicRanges_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_3.5.0zlibbioc_1.25.0uuid_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_0.2.0Matrix_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_0.2.4tidyr_0.8.0
> reshape2_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  
> 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 
> ), 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 

[Bioc-devel] Suggested edits to support site posting guide

[Michael Love]

dear all,

I've edited the text from the posting guide
 to update it a
bit.

For example, some of the text still referred to the mailing list
​: ​
"Compose a new message with a new subject line".

​Mostly, though, I wanted to emphasize posting all of their R code and
information about the experiment, which is often missing from support site
posts.​ The self-contained example with data and code is rarely possible
because many Bioc users have large datasets that can't be shared.
​
​Curious if this is useful or if others have suggestions. The following
link allows edits:​

https://docs.google.com/document/d/1baiBUYB8E02KMbaojjoo-
tKV3Ctd9sA5lVCvwFIWquA/edit?usp=sharing

​best,
Mike​

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Re: [Bioc-devel] iGraph depending packages failing on Windows build machines

[Obenchain, Valerie]

Petr,

Yesterday I installed R 3.5.0 beta on the devel Windows builder (tokay2). The 
report has not posted yet but I checked on the build of PharmacoGx and it is 
clean.

It looks like the CRAN 'maps' package was updated on April 4. It's possible 
that during the nightly builds, the new version of 'maps' was installed for x64 
arch only. The build system uses update.packages() to update CRAN dependencies. 
update.packages() may have picked up the source package because the Windows 
binary for the new version was not available yet which resulted in a x64-only 
installation of 'maps'.

We'll look into modifying in the build system code to handle this situation 
better. Thanks again for reporting it.

Valerie


On 04/10/2018 04:44 PM, petr smirnov wrote:

I noticed that our Bioconductor package (PharmacoGx) is failing to build on
Windows development, with the error:

 error: DLL 'maps' not found: maybe not installed for this architecture?

A google search brings up the package 'sincell', which has experienced this
error before.

The only dependency that package has is iGraph (CRAN), which we share with
them. Checking some of the build reports, there's a handful of packages
failing with the same issue.

There is also at least one package, 'Mulcom', that is failing with the
error:

Error : package 'maps' is not installed for 'arch = i386'

The CRAN package 'maps' seems to be the one providing the 'maps.dll' file.
There seems to be a successful binary build of the 'maps' package on CRAN
for both the release and prerelease versions of R.

Is this is an issue with the package 'maps' not being successfully
installed on the Windows build system?





This email message may contain legally privileged and/or confidential 
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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] Setup for pushing changes in unifiedWMWqPCR to bioconductor git.

[Joris Meys]

Hi all,

For the package unifiedWMWqPCR I want to push some updates on the
documentation, but apparently I don't have access to the bioconductor git
any longer. I had to completely reinstall my system here, so probably
either my key got lost, or I'm using the wrong account to push.

I tried to find out what key and user was registered, but couldn't find it.
Hence a few questions:

- Is there any way to find out how I am registered today (i.e. name and
public key)?
- I'm JoFAM on github, but the repo is in an organization called
CenterForStatistics-UGent. What github name do I use then for sending a new
public key?
- I use my work email for maintaining the package, but my account is set to
my personal email. Is that a problem and if so, how should I tackle that?

Thank you in advance.

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
---
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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