[Bioc-devel] Add OrgDb class to slot, warning during build

Hello all,

#I have been attempting to create a slot in my own class foo that is
supposed to contain an OrgDb object from the AnnotationDbi-package.
Actually it works, but during my build I get this warning:

** R
** inst
** preparing package for lazy loading
Warning: Class "OrgDb" is defined (with package slot ?AnnotationDbi?) but
no metadata object found to revise superClass information---not exported?
Making a copy in package fooPackage

#Below the parts of the code that may be relevant to solve the problem.
#My AllClasses file contain these lines:
setClassUnion("OrgDbOrNULL", c("OrgDb","NULL"))
setClass("foo",representation(

             OrgDb="OrgDbOrNULL",
             TxDbUCSC="TranscriptDbOrNULL"

             )
)

#My NAMESPACE file contain these lines:
importClassesFrom(AnnotationDbi, AnnotationDb)
importClassesFrom(GenomicFeatures, TranscriptDb)

#My DESCRIPTION file contain these lines:
Depends: R (>= 2.15.1), AnnotationDbi
Imports: methods, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures,
Rsamtools, AnnotationDbi


#To add the TranscriptDb works perfectly(no warnings during build), but not
the AnnotationDb. I have looked at the source code for AnnotationDb and
realized it has reference classes. This might be causing the warning during
build, of the reason that I cannot import the OrgDb class in NAMESPACE, and
that because it is not exported from AnnotationDbi. Thought putting it in
the Depends field in the DESCRIPTION would help, but it did not,
unfortunately. All kinds of help is appreciated.

Sincerely,
Jesper

sessionInfo()

R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] basicASE_1.3         AnnotationDbi_1.18.4 Biobase_2.16.0
[4] BiocGenerics_0.2.0

loaded via a namespace (and not attached):
  [1] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
  [4] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
  [7] GenomicRanges_1.8.13  IRanges_1.14.4        RCurl_1.95-3
[10] Rsamtools_1.8.6       RSQLite_0.11.2        rtracklayer_1.16.3
[13] stats4_2.15.1         tools_2.15.1          XML_3.95-0.1
[16] zlibbioc_1.2.0

	[[alternative HTML version deleted]]

Thanks!

That helped the problem with the OrgDb warning. Unfortunately when I installed
the devel AnnotationDbi and BiocGenerics, I got around 40 other warnings during
the R CMD INSTALL , looking like this:

** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
   A specification for S3 class ?AsIs? in package ?IRanges? seems equivalent to
one from package ?BiocGenerics? and is not turning on duplicate class
definitions for this class
Warning: multiple methods tables found for ?sort?
Warning: multiple methods tables found for ?rank?
Warning: multiple methods tables found for ?as.data.frame?
Warning: multiple methods tables found for ?unlist?
Warning: multiple methods tables found for ?match?
Warning: replacing previous import ?.__C__AsIs? when loading ?IRanges?
Warning: replacing previous import ?as.data.frame? when loading ?IRanges?
Warning: replacing previous import ?match? when loading ?IRanges?
Warning: replacing previous import ?rank? when loading ?IRanges?
...
...

Can it be helped? And am very curious also to why all these warnings?

Jesper

NEW SESSIONINFO

 > sessionInfo()

R version 2.15.1 (2012-06-22)

Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] basicASE_1.3

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.21.9  Biobase_2.16.0        BiocGenerics_0.5.6
  [4] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
  [7] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
[10] GenomicRanges_1.8.13  IRanges_1.14.4        parallel_2.15.1
[13] RCurl_1.95-3          Rsamtools_1.8.6       RSQLite_0.11.2
[16] rtracklayer_1.16.3    stats4_2.15.1         tools_2.15.1
[19] XML_3.95-0.1          zlibbioc_1.2.0

 >

On Sun, Dec 23, 2012 at 8:06 AM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:

    Hi Jesper --


    On 12/22/2012 05:09 PM, Jesper G?din wrote:

        Hello all,

        #I have been attempting to create a slot in my own class foo that is
        supposed to contain an OrgDb object from the AnnotationDbi-package.
        Actually it works, but during my build I get this warning:

        ** R
        ** inst
        ** preparing package for lazy loading
        Warning: Class "OrgDb" is defined (with package slot ?AnnotationDbi?) but
        no metadata object found to revise superClass information---not exported?
        Making a copy in package fooPackage

        #Below the parts of the code that may be relevant to solve the problem.
        #My AllClasses file contain these lines:
        setClassUnion("OrgDbOrNULL", c("OrgDb","NULL"))
        setClass("foo",representation(

                      OrgDb="OrgDbOrNULL",
                      TxDbUCSC="TranscriptDbOrNULL"

                      )
        )

        #My NAMESPACE file contain these lines:
        importClassesFrom(__AnnotationDbi, AnnotationDb)
        importClassesFrom(__GenomicFeatures, TranscriptDb)

        #My DESCRIPTION file contain these lines:
        Depends: R (>= 2.15.1), AnnotationDbi
        Imports: methods, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures,
        Rsamtools, AnnotationDbi


        #To add the TranscriptDb works perfectly(no warnings during build), but not
        the AnnotationDb. I have looked at the source code for AnnotationDb and
        realized it has reference classes. This might be causing the warning during
        build, of the reason that I cannot import the OrgDb class in NAMESPACE, and
        that because it is not exported from AnnotationDbi. Thought putting it in
        the Depends field in the DESCRIPTION would help, but it did not,
        unfortunately. All kinds of help is appreciated.


    Thanks for reporting this. I have updated AnnotationDbi to export the OrgDb
    class. This is in AnnotationDbi 1.21.9, in the 'devel' version of
    Bioconductor (available when using the devel version of R). Version 1.21.9
    will be available with biocLite after about 10am PST Monday.

    You will also need to add

       importClassesFrom(__AnnotationDbi, AnnotationDb, OrgDb)

    to your NAMESAPCE.

    Best,

    Martin


        Sincerely,
        Jesper


            sessionInfo()

        R version 2.15.1 (2012-06-22)
        Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

        other attached packages:
        [1] basicASE_1.3         AnnotationDbi_1.18.4 Biobase_2.16.0
        [4] BiocGenerics_0.2.0

        loaded via a namespace (and not attached):
           [1] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
           [4] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
           [7] GenomicRanges_1.8.13  IRanges_1.14.4        RCurl_1.95-3
        [10] Rsamtools_1.8.6       RSQLite_0.11.2        rtracklayer_1.16.3
        [13] stats4_2.15.1         tools_2.15.1          XML_3.95-0.1
        [16] zlibbioc_1.2.0

                 [[alternative HTML version deleted]]

After some fighting I have now the bleeding edge of R and the bioconductor
packages, and my own package was installed without any errors. Perfect!

Even if I finally got everything to work I get this error worth mentioning:

biocLite("Biobase", type="source")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.9.6), R version 3.0.0.
Installing package(s) 'Biobase'
trying URL '
http://bioconductor.org/packages/2.12/bioc/src/contrib/Biobase_2.19.1.tar.gz
'
Content type 'application/x-gzip' length 1845259 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb

* installing *source* package ?Biobase? ...
** libs
gcc -std=gnu99 -I/home/<somepath>/r-devel/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
Rinit.c:3:31: fatal error: R_ext/RConverters.h: No such file or directory
compilation terminated.
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package ?Biobase?
* removing ?/home/<somepath>/r-devel/library/Biobase?
* restoring previous ?/home/<somepath>/r-devel/library/Biobase?

Instead I can install Biobase source by,
#"rdev" is my alias for r-devel

rdev CMD INSTALL Biobase -l $R_DEV_LIB

This is somehow weird...

/Jesper

sessionInfo()

R Under development (unstable) (2012-12-28 r61466)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] basicASE_1.3.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.21.9   Biobase_2.19.1         BiocGenerics_0.5.6
 [4] biomaRt_2.15.0         Biostrings_2.27.8      bitops_1.0-5
 [7] BSgenome_1.27.1        DBI_0.2-5              GenomicFeatures_1.11.5
[10] GenomicRanges_1.11.20  IRanges_1.17.23        parallel_3.0.0
[13] RCurl_1.95-3           Rsamtools_1.11.14      RSQLite_0.11.2
[16] rtracklayer_1.19.6     stats4_3.0.0           tools_3.0.0
[19] XML_3.95-0.1           zlibbioc_1.5.0



On Mon, Dec 24, 2012 at 2:18 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

On 12/23/2012 05:07 PM, Jesper G?din wrote:

Thanks!

That helped the problem with the OrgDb warning. Unfortunately when I
installed
the devel AnnotationDbi and BiocGenerics, I got around 40 other warnings
during
the R CMD INSTALL , looking like this:

** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
   A specification for S3 class ?AsIs? in package ?IRanges? seems
equivalent to
one from package ?BiocGenerics? and is not turning on duplicate class
definitions for this class
Warning: multiple methods tables found for ?sort?
Warning: multiple methods tables found for ?rank?
Warning: multiple methods tables found for ?as.data.frame?
Warning: multiple methods tables found for ?unlist?
Warning: multiple methods tables found for ?match?
Warning: replacing previous import ?.__C__AsIs? when loading ?IRanges?
Warning: replacing previous import ?as.data.frame? when loading ?IRanges?
Warning: replacing previous import ?match? when loading ?IRanges?
Warning: replacing previous import ?rank? when loading ?IRanges?
...
...

Can it be helped? And am very curious also to why all these warnings?

Jesper

NEW SESSIONINFO

 > sessionInfo()

R version 2.15.1 (2012-06-22)

You'll need to use R-devel aka R-3.0; this will likely mean 'starting from
scratch' with installing bioc packages, so they'll all then be up-to-date
and most (all?) of these warnings will go away. Right now, you have a mix
of 'devel' and release Bioc packages (note the even (release) and odd
(devel) 'y' part of the x.y.z version numbers in your Bioc packages), which
is a recipe for disaster. Some of the warnings might persist, but that's
life in the devel lanes -- there is some code re-organization going on at
the moment, and things may be in a temporary state of flux.

Martin

 Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] basicASE_1.3

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.21.9  Biobase_2.16.0        BiocGenerics_0.5.6
  [4] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
  [7] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
[10] GenomicRanges_1.8.13  IRanges_1.14.4        parallel_2.15.1
[13] RCurl_1.95-3          Rsamtools_1.8.6       RSQLite_0.11.2
[16] rtracklayer_1.16.3    stats4_2.15.1         tools_2.15.1
[19] XML_3.95-0.1          zlibbioc_1.2.0

 >

On Sun, Dec 23, 2012 at 8:06 AM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:

    Hi Jesper --


    On 12/22/2012 05:09 PM, Jesper G?din wrote:

        Hello all,

        #I have been attempting to create a slot in my own class foo that
is
        supposed to contain an OrgDb object from the
AnnotationDbi-package.
        Actually it works, but during my build I get this warning:

        ** R
        ** inst
        ** preparing package for lazy loading
        Warning: Class "OrgDb" is defined (with package slot
?AnnotationDbi?) but
        no metadata object found to revise superClass information---not
exported?
        Making a copy in package fooPackage

        #Below the parts of the code that may be relevant to solve the
problem.
        #My AllClasses file contain these lines:
        setClassUnion("OrgDbOrNULL", c("OrgDb","NULL"))
        setClass("foo",representation(

                      OrgDb="OrgDbOrNULL",
                      TxDbUCSC="TranscriptDbOrNULL"

                      )
        )

        #My NAMESPACE file contain these lines:
        importClassesFrom(__**AnnotationDbi, AnnotationDb)
        importClassesFrom(__**GenomicFeatures, TranscriptDb)


        #My DESCRIPTION file contain these lines:
        Depends: R (>= 2.15.1), AnnotationDbi
        Imports: methods, BiocGenerics, IRanges, GenomicRanges,
GenomicFeatures,
        Rsamtools, AnnotationDbi


        #To add the TranscriptDb works perfectly(no warnings during
build), but not
        the AnnotationDb. I have looked at the source code for
AnnotationDb and
        realized it has reference classes. This might be causing the
warning during
        build, of the reason that I cannot import the OrgDb class in
NAMESPACE, and
        that because it is not exported from AnnotationDbi. Thought
putting it in
        the Depends field in the DESCRIPTION would help, but it did not,
        unfortunately. All kinds of help is appreciated.


    Thanks for reporting this. I have updated AnnotationDbi to export the
OrgDb
    class. This is in AnnotationDbi 1.21.9, in the 'devel' version of
    Bioconductor (available when using the devel version of R). Version
1.21.9
    will be available with biocLite after about 10am PST Monday.

    You will also need to add

       importClassesFrom(__**AnnotationDbi, AnnotationDb, OrgDb)


    to your NAMESAPCE.

    Best,

    Martin


        Sincerely,
        Jesper


            sessionInfo()

        R version 2.15.1 (2012-06-22)
        Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

        other attached packages:
        [1] basicASE_1.3         AnnotationDbi_1.18.4 Biobase_2.16.0
        [4] BiocGenerics_0.2.0

        loaded via a namespace (and not attached):
           [1] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
           [4] BSgenome_1.24.0       DBI_0.2-5
GenomicFeatures_1.8.3
           [7] GenomicRanges_1.8.13  IRanges_1.14.4        RCurl_1.95-3
        [10] Rsamtools_1.8.6       RSQLite_0.11.2
 rtracklayer_1.16.3
        [13] stats4_2.15.1         tools_2.15.1          XML_3.95-0.1
        [16] zlibbioc_1.2.0

                 [[alternative HTML version deleted]]

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

        [[alternative HTML version deleted]]

Hi Dan,

Actually my $R_HOME is empty. But even if I would set $R_HOME to r-devel
directory the include/R_ext/ does not contain RConverters.h (only the files
specified below are present)

/R_ext$ ls
Applic.h
Arith.h
BLAS.h
Boolean.h
Callbacks.h
Complex.h
Constants.h
Error.h
GetX11Image.h
GraphicsDevice.h
GraphicsEngine.h
Lapack.h
Linpack.h
MathThreads.h
Memory.h
QuartzDevice.h
Parse.h
Print.h
PrtUtil.h
R-ftp-http.h
RS.h
Random.h
Rdynload.h
Riconv.h
RStartup.h
Utils.h
eventloop.h
libextern.h
rlocale.h
stats_package.h
stats_stubs.h
Visibility.h

Yes I was using the same version of "rdev" interactively as from command
line.

Notice, that I wasnt allowed to install Biobase from the command line at a
start, but with these commands after eachother then it worked:
(1)rdev CMD INSTALL Biobase -l $R_DEV_LIB #error
(2)R CMD INSTALL Biobase #No error
(3)R CMD INSTALL Biobase -l $R_DEV_LIB #error
(4)rdev CMD INSTALL Biobase -l $R_DEV_LIB #no error, same command as in (1)

Also notice that I have the RConverters.h located in
~/bin/R-2.15.1/include/R_ext/RConverters.h
/usr/local/lib64/R/include/R_ext/RConverters.h
/usr/share/R/include/R_ext/RConverters.h

Hope this helps :)

/Jesper


On Fri, Dec 28, 2012 at 8:31 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

On Fri, Dec 28, 2012 at 11:01 AM, Jesper G?din <jesper.gadin at gmail.com>
wrote:

After some fighting I have now the bleeding edge of R and the
bioconductor
packages, and my own package was installed without any errors. Perfect!

Even if I finally got everything to work I get this error worth
mentioning:

biocLite("Biobase", type="source")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.9.6), R version 3.0.0.
Installing package(s) 'Biobase'
trying URL '

http://bioconductor.org/packages/2.12/bioc/src/contrib/Biobase_2.19.1.tar.gz
'
Content type 'application/x-gzip' length 1845259 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb

* installing *source* package ?Biobase? ...
** libs
gcc -std=gnu99 -I/home/<somepath>/r-devel/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
Rinit.c:3:31: fatal error: R_ext/RConverters.h: No such file or
directory
compilation terminated.
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package ?Biobase?
* removing ?/home/<somepath>/r-devel/library/Biobase?
* restoring previous ?/home/<somepath>/r-devel/library/Biobase?

Hmm, this does seem somehow broken, Does the file
$R_HOME/include/R_ext/RConverters.h
exist?
Are you using the same version of R interactively as you are on the
command line (rdev)? If not, does this work when you do?

Dan

Instead I can install Biobase source by,
#"rdev" is my alias for r-devel

rdev CMD INSTALL Biobase -l $R_DEV_LIB

This is somehow weird...

/Jesper

sessionInfo()

R Under development (unstable) (2012-12-28 r61466)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] basicASE_1.3.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.21.9   Biobase_2.19.1         BiocGenerics_0.5.6
 [4] biomaRt_2.15.0         Biostrings_2.27.8      bitops_1.0-5
 [7] BSgenome_1.27.1        DBI_0.2-5
GenomicFeatures_1.11.5
[10] GenomicRanges_1.11.20  IRanges_1.17.23        parallel_3.0.0
[13] RCurl_1.95-3           Rsamtools_1.11.14      RSQLite_0.11.2
[16] rtracklayer_1.19.6     stats4_3.0.0           tools_3.0.0
[19] XML_3.95-0.1           zlibbioc_1.5.0



On Mon, Dec 24, 2012 at 2:18 AM, Martin Morgan <mtmorgan at fhcrc.org>
wrote:

On 12/23/2012 05:07 PM, Jesper G?din wrote:

Thanks!

That helped the problem with the OrgDb warning. Unfortunately when I
installed
the devel AnnotationDbi and BiocGenerics, I got around 40 other
warnings
during
the R CMD INSTALL , looking like this:

** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
   A specification for S3 class ?AsIs? in package ?IRanges? seems
equivalent to
one from package ?BiocGenerics? and is not turning on duplicate class
definitions for this class
Warning: multiple methods tables found for ?sort?
Warning: multiple methods tables found for ?rank?
Warning: multiple methods tables found for ?as.data.frame?
Warning: multiple methods tables found for ?unlist?
Warning: multiple methods tables found for ?match?
Warning: replacing previous import ?.__C__AsIs? when loading ?IRanges?
Warning: replacing previous import ?as.data.frame? when loading
?IRanges?
Warning: replacing previous import ?match? when loading ?IRanges?
Warning: replacing previous import ?rank? when loading ?IRanges?
...
...

Can it be helped? And am very curious also to why all these warnings?

Jesper

NEW SESSIONINFO

 > sessionInfo()

R version 2.15.1 (2012-06-22)

You'll need to use R-devel aka R-3.0; this will likely mean 'starting
from
scratch' with installing bioc packages, so they'll all then be
up-to-date
and most (all?) of these warnings will go away. Right now, you have a
mix
of 'devel' and release Bioc packages (note the even (release) and odd
(devel) 'y' part of the x.y.z version numbers in your Bioc packages),
which
is a recipe for disaster. Some of the warnings might persist, but
that's
life in the devel lanes -- there is some code re-organization going on
at
the moment, and things may be in a temporary state of flux.

Martin

 Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] basicASE_1.3

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.21.9  Biobase_2.16.0        BiocGenerics_0.5.6
  [4] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
  [7] BSgenome_1.24.0       DBI_0.2-5
GenomicFeatures_1.8.3
[10] GenomicRanges_1.8.13  IRanges_1.14.4        parallel_2.15.1
[13] RCurl_1.95-3          Rsamtools_1.8.6       RSQLite_0.11.2
[16] rtracklayer_1.16.3    stats4_2.15.1         tools_2.15.1
[19] XML_3.95-0.1          zlibbioc_1.2.0

 >

On Sun, Dec 23, 2012 at 8:06 AM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:

    Hi Jesper --


    On 12/22/2012 05:09 PM, Jesper G?din wrote:

        Hello all,

        #I have been attempting to create a slot in my own class foo
that
is
        supposed to contain an OrgDb object from the
AnnotationDbi-package.
        Actually it works, but during my build I get this warning:

        ** R
        ** inst
        ** preparing package for lazy loading
        Warning: Class "OrgDb" is defined (with package slot
?AnnotationDbi?) but
        no metadata object found to revise superClass
information---not
exported?
        Making a copy in package fooPackage

        #Below the parts of the code that may be relevant to solve the
problem.
        #My AllClasses file contain these lines:
        setClassUnion("OrgDbOrNULL", c("OrgDb","NULL"))
        setClass("foo",representation(

                      OrgDb="OrgDbOrNULL",
                      TxDbUCSC="TranscriptDbOrNULL"

                      )
        )

        #My NAMESPACE file contain these lines:
        importClassesFrom(__**AnnotationDbi, AnnotationDb)
        importClassesFrom(__**GenomicFeatures, TranscriptDb)


        #My DESCRIPTION file contain these lines:
        Depends: R (>= 2.15.1), AnnotationDbi
        Imports: methods, BiocGenerics, IRanges, GenomicRanges,
GenomicFeatures,
        Rsamtools, AnnotationDbi


        #To add the TranscriptDb works perfectly(no warnings during
build), but not
        the AnnotationDb. I have looked at the source code for
AnnotationDb and
        realized it has reference classes. This might be causing the
warning during
        build, of the reason that I cannot import the OrgDb class in
NAMESPACE, and
        that because it is not exported from AnnotationDbi. Thought
putting it in
        the Depends field in the DESCRIPTION would help, but it did
not,
        unfortunately. All kinds of help is appreciated.


    Thanks for reporting this. I have updated AnnotationDbi to export
the
OrgDb
    class. This is in AnnotationDbi 1.21.9, in the 'devel' version of
    Bioconductor (available when using the devel version of R).
Version
1.21.9
    will be available with biocLite after about 10am PST Monday.

    You will also need to add

       importClassesFrom(__**AnnotationDbi, AnnotationDb, OrgDb)


    to your NAMESAPCE.

    Best,

    Martin


        Sincerely,
        Jesper


            sessionInfo()

        R version 2.15.1 (2012-06-22)
        Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

        other attached packages:
        [1] basicASE_1.3         AnnotationDbi_1.18.4 Biobase_2.16.0
        [4] BiocGenerics_0.2.0

        loaded via a namespace (and not attached):
           [1] biomaRt_2.12.0        Biostrings_2.24.1
bitops_1.0-5
           [4] BSgenome_1.24.0       DBI_0.2-5
GenomicFeatures_1.8.3
           [7] GenomicRanges_1.8.13  IRanges_1.14.4
RCurl_1.95-3
        [10] Rsamtools_1.8.6       RSQLite_0.11.2
 rtracklayer_1.16.3
        [13] stats4_2.15.1         tools_2.15.1          XML_3.95-0.1
        [16] zlibbioc_1.2.0

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