[Bioc-devel] Found more than one class "Annotated" in cache

Dear list,

we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.

The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a dependency
of phylobase). Note that we want the former. This causes the following
message to be thrown every time we create a new object.

Found more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'


A minimal example is the following.

library(SummarizedExperiment)> SummarizedExperiment()class: SummarizedExperiment

dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):> library(phylobase)> SummarizedExperiment()Found
more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'class: SummarizedExperiment
dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):

sessionInfo()R Under development (unstable) (2016-03-07 r70284)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets  methods
[9] base

other attached packages:
[1] phylobase_0.8.2             SummarizedExperiment_1.1.21
[3] Biobase_2.31.3              GenomicRanges_1.23.23
[5] GenomeInfoDb_1.7.6          IRanges_2.5.39
[7] S4Vectors_0.9.41            BiocGenerics_0.17.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3      plyr_1.8.3       XVector_0.11.7   iterators_1.0.8
 [5] tools_3.3.0      zlibbioc_1.17.0  uuid_0.1-2       jsonlite_0.9.19
 [9] nlme_3.1-125     lattice_0.20-33  foreach_1.4.3    DBI_0.3.1
[13] httr_1.1.0       stringr_1.0.0    dplyr_0.4.3      xml2_0.1.2
[17] ade4_1.7-4       grid_3.3.0       rredlist_0.1.0   reshape_0.8.5
[21] data.table_1.9.6 R6_2.1.2         XML_3.98-1.4     RNeXML_2.0.6
[25] reshape2_1.4.1   tidyr_0.4.1      magrittr_1.5     codetools_0.2-14
[29] assertthat_0.1   bold_0.3.5       taxize_0.7.5     ape_3.4
[33] stringi_1.0-1    rncl_0.6.0       lazyeval_0.1.10  rotl_0.5.0
[37] chron_2.3-47


Since we need to import both packages, is there a way to explicitly use the
correct definition of "Annotated" or to not import the class "Annotated"
from RNeXML?

Or is this something that could be addressed in the SummarizedExperiment
package?

These are our DESCRIPTION and NAMESPACE file (note that we are importing
only what we need from phylobase):
https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE

See also Henrik's comment at:
https://github.com/epurdom/clusterExperiment/issues/66

Thank you in advance for any help!

Best,
davide

        [[alternative HTML version deleted]]

Yea, this is a bug in R, in my opinion. The class cache circumvents
the namespace imports. In my working copy I've fixed it by falling
back to the namespace search when there are multiple hits. That at
least fixes this case.

You can disable the message in the short term by setting the
"getClass.msg" option to FALSE.

Michael

On Sun, Apr 24, 2016 at 12:50 PM, davide risso <risso.davide at gmail.com> wrote:

Dear list,

we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.

The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a dependency
of phylobase). Note that we want the former. This causes the following
message to be thrown every time we create a new object.

Found more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'


A minimal example is the following.

library(SummarizedExperiment)> SummarizedExperiment()class: SummarizedExperiment

dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):> library(phylobase)> SummarizedExperiment()Found
more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'class: SummarizedExperiment
dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):

sessionInfo()R Under development (unstable) (2016-03-07 r70284)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets  methods
[9] base

other attached packages:
[1] phylobase_0.8.2             SummarizedExperiment_1.1.21
[3] Biobase_2.31.3              GenomicRanges_1.23.23
[5] GenomeInfoDb_1.7.6          IRanges_2.5.39
[7] S4Vectors_0.9.41            BiocGenerics_0.17.3

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.3      plyr_1.8.3       XVector_0.11.7   iterators_1.0.8
  [5] tools_3.3.0      zlibbioc_1.17.0  uuid_0.1-2       jsonlite_0.9.19
  [9] nlme_3.1-125     lattice_0.20-33  foreach_1.4.3    DBI_0.3.1
[13] httr_1.1.0       stringr_1.0.0    dplyr_0.4.3      xml2_0.1.2
[17] ade4_1.7-4       grid_3.3.0       rredlist_0.1.0   reshape_0.8.5
[21] data.table_1.9.6 R6_2.1.2         XML_3.98-1.4     RNeXML_2.0.6
[25] reshape2_1.4.1   tidyr_0.4.1      magrittr_1.5     codetools_0.2-14
[29] assertthat_0.1   bold_0.3.5       taxize_0.7.5     ape_3.4
[33] stringi_1.0-1    rncl_0.6.0       lazyeval_0.1.10  rotl_0.5.0
[37] chron_2.3-47


Since we need to import both packages, is there a way to explicitly use the
correct definition of "Annotated" or to not import the class "Annotated"
from RNeXML?

Or is this something that could be addressed in the SummarizedExperiment
package?

These are our DESCRIPTION and NAMESPACE file (note that we are importing
only what we need from phylobase):
https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE

See also Henrik's comment at:
https://github.com/epurdom/clusterExperiment/issues/66

Thank you in advance for any help!

Best,
davide

         [[alternative HTML version deleted]]

On 04/25/2016 03:53 PM, Michael Lawrence wrote:

Yea, this is a bug in R, in my opinion. The class cache circumvents
the namespace imports. In my working copy I've fixed it by falling
back to the namespace search when there are multiple hits. That at
least fixes this case.

This also fixes it

Index: src/library/methods/R/SClasses.R
===================================================================
--- src/library/methods/R/SClasses.R    (revision 70547)
+++ src/library/methods/R/SClasses.R    (working copy)
@@ -524,7 +524,7 @@
        superClass <- exti at superClass
        if(!exti at simple && !is(object, superClass))
            next ## skip conditional relations that don't hold for this
object
-       superDef <- getClassDef(superClass, where = where)
+       superDef <- getClassDef(superClass, package = packageSlot(exti))
        if(is.null(superDef)) {
            errors <- c(errors,
                        paste0("superclass \"", superClass,


There's another problem seen by loading the packages in reverse order

suppressPackageStartupMessages({ library(RNeXML); library(GenomicRanges)
})

Found more than one class "Annotated" in cache; using the first, from
namespace 'RNeXML'
Also defined by 'S4Vectors'
...

which is from

[[17]]
S4Vectors:::setDefaultSlotValue("XRaw", "shared", new("SharedRaw"),
    where = asNamespace(pkgname))

[[18]]
resetClass(classname, classdef, where = where)

[[19]]
completeClassDefinition(Class, classDef, where)

[[20]]
.completeClassSlots(ClassDef, where)

[[21]]
isClass(eClass, where = where)

[[22]]
getClassDef(Class, where)

[[23]]
.getClassFromCache(Class, where, package = package, resolve.msg =
resolve.msg)

but I haven't quite got to the bottom of that. Also, I think these are both
different from but related to

suppressPackageStartupMessages(library(Statomica))

Error in .mergeMethodsTable(generic, mtable, tt, attach) :
  trying to get slot "defined" from an object of a basic class ("list") with
no slots
Error: package or namespace load failed for 'Statomica'

You can disable the message in the short term by setting the
"getClass.msg" option to FALSE.

Michael

On Sun, Apr 24, 2016 at 12:50 PM, davide risso <risso.davide at gmail.com>
wrote:

Dear list,

we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.

The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a
dependency
of phylobase). Note that we want the former. This causes the following
message to be thrown every time we create a new object.

Found more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'


A minimal example is the following.

library(SummarizedExperiment)> SummarizedExperiment()class:
SummarizedExperiment

dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):> library(phylobase)> SummarizedExperiment()Found
more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'class: SummarizedExperiment
dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):

sessionInfo()R Under development (unstable) (2016-03-07 r70284)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets  methods
[9] base

other attached packages:
[1] phylobase_0.8.2             SummarizedExperiment_1.1.21
[3] Biobase_2.31.3              GenomicRanges_1.23.23
[5] GenomeInfoDb_1.7.6          IRanges_2.5.39
[7] S4Vectors_0.9.41            BiocGenerics_0.17.3

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.3      plyr_1.8.3       XVector_0.11.7   iterators_1.0.8
  [5] tools_3.3.0      zlibbioc_1.17.0  uuid_0.1-2       jsonlite_0.9.19
  [9] nlme_3.1-125     lattice_0.20-33  foreach_1.4.3    DBI_0.3.1
[13] httr_1.1.0       stringr_1.0.0    dplyr_0.4.3      xml2_0.1.2
[17] ade4_1.7-4       grid_3.3.0       rredlist_0.1.0   reshape_0.8.5
[21] data.table_1.9.6 R6_2.1.2         XML_3.98-1.4     RNeXML_2.0.6
[25] reshape2_1.4.1   tidyr_0.4.1      magrittr_1.5     codetools_0.2-14
[29] assertthat_0.1   bold_0.3.5       taxize_0.7.5     ape_3.4
[33] stringi_1.0-1    rncl_0.6.0       lazyeval_0.1.10  rotl_0.5.0
[37] chron_2.3-47


Since we need to import both packages, is there a way to explicitly use
the
correct definition of "Annotated" or to not import the class "Annotated"
from RNeXML?

Or is this something that could be addressed in the SummarizedExperiment
package?

These are our DESCRIPTION and NAMESPACE file (note that we are importing
only what we need from phylobase):
https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE

See also Henrik's comment at:
https://github.com/epurdom/clusterExperiment/issues/66

Thank you in advance for any help!

Best,
davide

         [[alternative HTML version deleted]]

This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or
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distribution, or use of this email message is prohibited.  If you have
received this message in error, please notify the sender immediately by
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Yes, that's a better fix for this in principle, since it uses the
information encoded in the extends object, although I think
getClassFromCache() also needs to be fixed, so that getClassDef() sees
only the imported classes when only given "where". That's a more
general fix that works in both load orders.

Maybe the superClass slot of the extends object should store its
package? Would be convenient, if somewhat redundant. Conceptually, it
seems the package really belongs on superClass, not on the extends
object itself (how does a ClassExtends pertain to a package?).

Index: ClassExtensions.R
===================================================================
--- ClassExtensions.R (revision 70547)
+++ ClassExtensions.R (working copy)
@@ -316,6 +316,7 @@
         stop(gettextf("the 'replace' argument to setIs() should be a
function of 2 or 3 arguments, got an object of class %s",
                       dQuote(class(replace))), domain = NA)

+    packageSlot(to) <- package
     new(extClass, subClass = Class, superClass = to, package = package,
  coerce = coerce, test = test, replace = replace, simple = simple,
  by = by, dataPart = dataPart, distance = distance)



On Mon, Apr 25, 2016 at 1:24 PM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:

On 04/25/2016 03:53 PM, Michael Lawrence wrote:

Yea, this is a bug in R, in my opinion. The class cache circumvents
the namespace imports. In my working copy I've fixed it by falling
back to the namespace search when there are multiple hits. That at
least fixes this case.

This also fixes it

Index: src/library/methods/R/SClasses.R
===================================================================
--- src/library/methods/R/SClasses.R    (revision 70547)
+++ src/library/methods/R/SClasses.R    (working copy)
@@ -524,7 +524,7 @@
        superClass <- exti at superClass
        if(!exti at simple && !is(object, superClass))
            next ## skip conditional relations that don't hold for this
object
-       superDef <- getClassDef(superClass, where = where)
+       superDef <- getClassDef(superClass, package = packageSlot(exti))
        if(is.null(superDef)) {
            errors <- c(errors,
                        paste0("superclass \"", superClass,


There's another problem seen by loading the packages in reverse order

suppressPackageStartupMessages({ library(RNeXML); library(GenomicRanges)
})

Found more than one class "Annotated" in cache; using the first, from
namespace 'RNeXML'
Also defined by 'S4Vectors'
...

which is from

[[17]]
S4Vectors:::setDefaultSlotValue("XRaw", "shared", new("SharedRaw"),
    where = asNamespace(pkgname))

[[18]]
resetClass(classname, classdef, where = where)

[[19]]
completeClassDefinition(Class, classDef, where)

[[20]]
.completeClassSlots(ClassDef, where)

[[21]]
isClass(eClass, where = where)

[[22]]
getClassDef(Class, where)

[[23]]
.getClassFromCache(Class, where, package = package, resolve.msg =
resolve.msg)

but I haven't quite got to the bottom of that. Also, I think these are

both

different from but related to

suppressPackageStartupMessages(library(Statomica))

Error in .mergeMethodsTable(generic, mtable, tt, attach) :
  trying to get slot "defined" from an object of a basic class ("list")

with

no slots
Error: package or namespace load failed for 'Statomica'

You can disable the message in the short term by setting the
"getClass.msg" option to FALSE.

Michael

On Sun, Apr 24, 2016 at 12:50 PM, davide risso <risso.davide at gmail.com>
wrote:

Dear list,

we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.

The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a
dependency
of phylobase). Note that we want the former. This causes the following
message to be thrown every time we create a new object.

Found more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'


A minimal example is the following.

library(SummarizedExperiment)> SummarizedExperiment()class:
SummarizedExperiment

dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):> library(phylobase)> SummarizedExperiment()Found
more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'class: SummarizedExperiment
dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):

sessionInfo()R Under development (unstable) (2016-03-07 r70284)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets  methods
[9] base

other attached packages:
[1] phylobase_0.8.2             SummarizedExperiment_1.1.21
[3] Biobase_2.31.3              GenomicRanges_1.23.23
[5] GenomeInfoDb_1.7.6          IRanges_2.5.39
[7] S4Vectors_0.9.41            BiocGenerics_0.17.3

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.3      plyr_1.8.3       XVector_0.11.7

 iterators_1.0.8

  [5] tools_3.3.0      zlibbioc_1.17.0  uuid_0.1-2

 jsonlite_0.9.19

  [9] nlme_3.1-125     lattice_0.20-33  foreach_1.4.3    DBI_0.3.1
[13] httr_1.1.0       stringr_1.0.0    dplyr_0.4.3      xml2_0.1.2
[17] ade4_1.7-4       grid_3.3.0       rredlist_0.1.0   reshape_0.8.5
[21] data.table_1.9.6 R6_2.1.2         XML_3.98-1.4     RNeXML_2.0.6
[25] reshape2_1.4.1   tidyr_0.4.1      magrittr_1.5

 codetools_0.2-14

[29] assertthat_0.1   bold_0.3.5       taxize_0.7.5     ape_3.4
[33] stringi_1.0-1    rncl_0.6.0       lazyeval_0.1.10  rotl_0.5.0
[37] chron_2.3-47


Since we need to import both packages, is there a way to explicitly use
the
correct definition of "Annotated" or to not import the class

"Annotated"

from RNeXML?

Or is this something that could be addressed in the

SummarizedExperiment

package?

These are our DESCRIPTION and NAMESPACE file (note that we are

importing

only what we need from phylobase):
https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE

See also Henrik's comment at:
https://github.com/epurdom/clusterExperiment/issues/66

Thank you in advance for any help!

Best,
davide

         [[alternative HTML version deleted]]

This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee

or

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 delete this email message from your computer. Thank you.

Thank you Michael and Martin for looking into this!

Best,
davide


On Mon, Apr 25, 2016 at 1:49 PM Michael Lawrence <
lawrence.michael at gene.com> wrote:

Yes, that's a better fix for this in principle, since it uses the
information encoded in the extends object, although I think
getClassFromCache() also needs to be fixed, so that getClassDef() sees
only the imported classes when only given "where". That's a more
general fix that works in both load orders.

Maybe the superClass slot of the extends object should store its
package? Would be convenient, if somewhat redundant. Conceptually, it
seems the package really belongs on superClass, not on the extends
object itself (how does a ClassExtends pertain to a package?).

Index: ClassExtensions.R
===================================================================
--- ClassExtensions.R (revision 70547)
+++ ClassExtensions.R (working copy)
@@ -316,6 +316,7 @@
         stop(gettextf("the 'replace' argument to setIs() should be a
function of 2 or 3 arguments, got an object of class %s",
                       dQuote(class(replace))), domain = NA)

+    packageSlot(to) <- package
     new(extClass, subClass = Class, superClass = to, package = package,
  coerce = coerce, test = test, replace = replace, simple = simple,
  by = by, dataPart = dataPart, distance = distance)



On Mon, Apr 25, 2016 at 1:24 PM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:

On 04/25/2016 03:53 PM, Michael Lawrence wrote:

Yea, this is a bug in R, in my opinion. The class cache circumvents
the namespace imports. In my working copy I've fixed it by falling
back to the namespace search when there are multiple hits. That at
least fixes this case.

This also fixes it

Index: src/library/methods/R/SClasses.R
===================================================================
--- src/library/methods/R/SClasses.R    (revision 70547)
+++ src/library/methods/R/SClasses.R    (working copy)
@@ -524,7 +524,7 @@
        superClass <- exti at superClass
        if(!exti at simple && !is(object, superClass))
            next ## skip conditional relations that don't hold for this
object
-       superDef <- getClassDef(superClass, where = where)
+       superDef <- getClassDef(superClass, package = packageSlot(exti))
        if(is.null(superDef)) {
            errors <- c(errors,
                        paste0("superclass \"", superClass,


There's another problem seen by loading the packages in reverse order

suppressPackageStartupMessages({ library(RNeXML);

library(GenomicRanges)

})

Found more than one class "Annotated" in cache; using the first, from
namespace 'RNeXML'
Also defined by 'S4Vectors'
...

which is from

[[17]]
S4Vectors:::setDefaultSlotValue("XRaw", "shared", new("SharedRaw"),
    where = asNamespace(pkgname))

[[18]]
resetClass(classname, classdef, where = where)

[[19]]
completeClassDefinition(Class, classDef, where)

[[20]]
.completeClassSlots(ClassDef, where)

[[21]]
isClass(eClass, where = where)

[[22]]
getClassDef(Class, where)

[[23]]
.getClassFromCache(Class, where, package = package, resolve.msg =
resolve.msg)

but I haven't quite got to the bottom of that. Also, I think these are

both

different from but related to

suppressPackageStartupMessages(library(Statomica))

Error in .mergeMethodsTable(generic, mtable, tt, attach) :
  trying to get slot "defined" from an object of a basic class ("list")

with

no slots
Error: package or namespace load failed for 'Statomica'

You can disable the message in the short term by setting the
"getClass.msg" option to FALSE.

Michael

On Sun, Apr 24, 2016 at 12:50 PM, davide risso <risso.davide at gmail.com

wrote:

Dear list,

we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.

The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a
dependency
of phylobase). Note that we want the former. This causes the following
message to be thrown every time we create a new object.

Found more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'


A minimal example is the following.

library(SummarizedExperiment)> SummarizedExperiment()class:
SummarizedExperiment

dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):> library(phylobase)> SummarizedExperiment()Found
more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'class: SummarizedExperiment
dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):

sessionInfo()R Under development (unstable) (2016-03-07 r70284)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets  methods
[9] base

other attached packages:
[1] phylobase_0.8.2             SummarizedExperiment_1.1.21
[3] Biobase_2.31.3              GenomicRanges_1.23.23
[5] GenomeInfoDb_1.7.6          IRanges_2.5.39
[7] S4Vectors_0.9.41            BiocGenerics_0.17.3

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.3      plyr_1.8.3       XVector_0.11.7

 iterators_1.0.8

  [5] tools_3.3.0      zlibbioc_1.17.0  uuid_0.1-2

 jsonlite_0.9.19

  [9] nlme_3.1-125     lattice_0.20-33  foreach_1.4.3    DBI_0.3.1
[13] httr_1.1.0       stringr_1.0.0    dplyr_0.4.3      xml2_0.1.2
[17] ade4_1.7-4       grid_3.3.0       rredlist_0.1.0   reshape_0.8.5
[21] data.table_1.9.6 R6_2.1.2         XML_3.98-1.4     RNeXML_2.0.6
[25] reshape2_1.4.1   tidyr_0.4.1      magrittr_1.5

 codetools_0.2-14

[29] assertthat_0.1   bold_0.3.5       taxize_0.7.5     ape_3.4
[33] stringi_1.0-1    rncl_0.6.0       lazyeval_0.1.10  rotl_0.5.0
[37] chron_2.3-47


Since we need to import both packages, is there a way to explicitly

use

the
correct definition of "Annotated" or to not import the class

"Annotated"

from RNeXML?

Or is this something that could be addressed in the

SummarizedExperiment

package?

These are our DESCRIPTION and NAMESPACE file (note that we are

importing

only what we need from phylobase):
https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE

See also Henrik's comment at:
https://github.com/epurdom/clusterExperiment/issues/66

Thank you in advance for any help!

Best,
davide

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Hi all,

when running R CMD check on our package, we get the following warning:

checking whether the namespace can be unloaded cleanly ... WARNING
---- unloading
Error in .getClassFromCache(what, resolve.confl = "all") :
  argument "where" is missing, with no default
Calls: unloadNamespace ... <Anonymous> -> .removeSuperclassBackRefs ->
.getClassFromCache
Execution halted

Is this warning related to the message mentioned earlier in this thread? If
so, should I expect this warning to go away once the bug in the class import
is fixed?

Here for the full Travis CI report:
https://travis-ci.org/epurdom/clusterExperiment/builds/126175973

Thanks,
Davide


On Mon, Apr 25, 2016 at 2:00 PM davide risso <risso.davide at gmail.com> wrote:

Thank you Michael and Martin for looking into this!

Best,
davide


On Mon, Apr 25, 2016 at 1:49 PM Michael Lawrence
<lawrence.michael at gene.com> wrote:

Yes, that's a better fix for this in principle, since it uses the
information encoded in the extends object, although I think
getClassFromCache() also needs to be fixed, so that getClassDef() sees
only the imported classes when only given "where". That's a more
general fix that works in both load orders.

Maybe the superClass slot of the extends object should store its
package? Would be convenient, if somewhat redundant. Conceptually, it
seems the package really belongs on superClass, not on the extends
object itself (how does a ClassExtends pertain to a package?).

Index: ClassExtensions.R
===================================================================
--- ClassExtensions.R (revision 70547)
+++ ClassExtensions.R (working copy)
@@ -316,6 +316,7 @@
         stop(gettextf("the 'replace' argument to setIs() should be a
function of 2 or 3 arguments, got an object of class %s",
                       dQuote(class(replace))), domain = NA)

+    packageSlot(to) <- package
     new(extClass, subClass = Class, superClass = to, package = package,
  coerce = coerce, test = test, replace = replace, simple = simple,
  by = by, dataPart = dataPart, distance = distance)



On Mon, Apr 25, 2016 at 1:24 PM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:

On 04/25/2016 03:53 PM, Michael Lawrence wrote:

Yea, this is a bug in R, in my opinion. The class cache circumvents
the namespace imports. In my working copy I've fixed it by falling
back to the namespace search when there are multiple hits. That at
least fixes this case.

This also fixes it

Index: src/library/methods/R/SClasses.R
===================================================================
--- src/library/methods/R/SClasses.R    (revision 70547)
+++ src/library/methods/R/SClasses.R    (working copy)
@@ -524,7 +524,7 @@
        superClass <- exti at superClass
        if(!exti at simple && !is(object, superClass))
            next ## skip conditional relations that don't hold for this
object
-       superDef <- getClassDef(superClass, where = where)
+       superDef <- getClassDef(superClass, package =
packageSlot(exti))
        if(is.null(superDef)) {
            errors <- c(errors,
                        paste0("superclass \"", superClass,


There's another problem seen by loading the packages in reverse order

suppressPackageStartupMessages({ library(RNeXML);
library(GenomicRanges)
})

Found more than one class "Annotated" in cache; using the first, from
namespace 'RNeXML'
Also defined by 'S4Vectors'
...

which is from

[[17]]
S4Vectors:::setDefaultSlotValue("XRaw", "shared", new("SharedRaw"),
    where = asNamespace(pkgname))

[[18]]
resetClass(classname, classdef, where = where)

[[19]]
completeClassDefinition(Class, classDef, where)

[[20]]
.completeClassSlots(ClassDef, where)

[[21]]
isClass(eClass, where = where)

[[22]]
getClassDef(Class, where)

[[23]]
.getClassFromCache(Class, where, package = package, resolve.msg =
resolve.msg)

but I haven't quite got to the bottom of that. Also, I think these are
both
different from but related to

suppressPackageStartupMessages(library(Statomica))

Error in .mergeMethodsTable(generic, mtable, tt, attach) :
  trying to get slot "defined" from an object of a basic class ("list")
with
no slots
Error: package or namespace load failed for 'Statomica'

You can disable the message in the short term by setting the
"getClass.msg" option to FALSE.

Michael

On Sun, Apr 24, 2016 at 12:50 PM, davide risso
<risso.davide at gmail.com>
wrote:

Dear list,

we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.

The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a
dependency
of phylobase). Note that we want the former. This causes the
following
message to be thrown every time we create a new object.

Found more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'


A minimal example is the following.

library(SummarizedExperiment)> SummarizedExperiment()class:
SummarizedExperiment

dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):> library(phylobase)> SummarizedExperiment()Found
more than one class "Annotated" in cache; using the first, from
namespace 'S4Vectors'class: SummarizedExperiment
dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):

sessionInfo()R Under development (unstable) (2016-03-07 r70284)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets  methods
[9] base

other attached packages:
[1] phylobase_0.8.2             SummarizedExperiment_1.1.21
[3] Biobase_2.31.3              GenomicRanges_1.23.23
[5] GenomeInfoDb_1.7.6          IRanges_2.5.39
[7] S4Vectors_0.9.41            BiocGenerics_0.17.3

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.3      plyr_1.8.3       XVector_0.11.7
iterators_1.0.8
  [5] tools_3.3.0      zlibbioc_1.17.0  uuid_0.1-2
jsonlite_0.9.19
  [9] nlme_3.1-125     lattice_0.20-33  foreach_1.4.3    DBI_0.3.1
[13] httr_1.1.0       stringr_1.0.0    dplyr_0.4.3      xml2_0.1.2
[17] ade4_1.7-4       grid_3.3.0       rredlist_0.1.0   reshape_0.8.5
[21] data.table_1.9.6 R6_2.1.2         XML_3.98-1.4     RNeXML_2.0.6
[25] reshape2_1.4.1   tidyr_0.4.1      magrittr_1.5
codetools_0.2-14
[29] assertthat_0.1   bold_0.3.5       taxize_0.7.5     ape_3.4
[33] stringi_1.0-1    rncl_0.6.0       lazyeval_0.1.10  rotl_0.5.0
[37] chron_2.3-47


Since we need to import both packages, is there a way to explicitly
use
the
correct definition of "Annotated" or to not import the class
"Annotated"
from RNeXML?

Or is this something that could be addressed in the
SummarizedExperiment
package?

These are our DESCRIPTION and NAMESPACE file (note that we are
importing
only what we need from phylobase):
https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE

See also Henrik's comment at:
https://github.com/epurdom/clusterExperiment/issues/66

Thank you in advance for any help!

Best,
davide

         [[alternative HTML version deleted]]

This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee
or
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 delete this email message from your computer. Thank you.