Re: [Bioc-devel] Missed change in S4Vectors
Sorry, that should say once I made the proposed change to "S4Vectors", not
"IRanges".
On Tue, 11 Aug 2015 8:51 am Peter Hickey wrote:
> Hi Hervé,
>
>
> Hmm, sorry I may have misdiagnosed my problem. I was having problems with
> some code in the bsseq vignette.
>
>
> The following demonstrates what was happening:
>
>
> > suppressPackageStartupMessages(library(bsseq))
>
> Warning message:
>
> In .recacheSubclasses(def@className, def, doSubclasses, env) :
>
> undefined subclass "externalRefMethod" of class "expressionORfunction";
> definition not updated
>
> > data(BS.chr22)
>
> > head(seqnames(BS.chr22), n = 4)
>
> factor-Rle of length 4 with 1 run
>
> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>
> object 'labeledLine' not found
>
> > sessionInfo()
>
> R version 3.2.1 (2015-06-18)
>
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>
> Running under: OS X 10.10.4 (Yosemite)
>
>
> locale:
>
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
>
> attached base packages:
>
> [1] stats4parallel stats graphics grDevices utils datasets
>
> [8] methods base
>
>
> other attached packages:
>
> [1] bsseq_1.5.5SummarizedExperiment_0.3.3
>
> [3] Biobase_2.29.1 GenomicRanges_1.21.18
>
> [5] GenomeInfoDb_1.5.10IRanges_2.3.18
>
> [7] S4Vectors_0.7.12 matrixStats_0.14.2
>
> [9] BiocGenerics_0.15.6
>
>
> loaded via a namespace (and not attached):
>
> [1] locfit_1.5-9.1 Rcpp_0.12.0 lattice_0.20-33 gtools_3.5.0
>
> [5] chron_2.3-47 plyr_1.8.3 grid_3.2.1 magrittr_1.5
>
> [9] scales_0.2.5 stringi_0.5-5reshape2_1.4.1 XVector_0.9.1
>
> [13] data.table_1.9.4 tools_3.2.1 stringr_1.0.0munsell_0.4.2
>
> [17] colorspace_1.2-6
>
>
> Once I made that proposed change to IRanges (locally) and re-install then
> it works as expected.
>
>
> Any ideas what I'm doing wrong?
>
>
> Thanks,
>
> Pete
>
>
>
> Hi Peter,
>
>
> Starting with S4Vectors 0.7.12, labeledLine() belongs to S4Vectors so
>
> using the triple colon should not be necessary (and doing so will
>
> actually trigger a note from R CMD check). Can you provide more
>
> details on why you need this?
>
>
> Thanks,
>
> H.
>
>
>
> On 08/09/2015 09:16 PM, Peter Hickey wrote:
>
> Hi Hervé,
>
>
> I was having trouble with some devel code of mine and tracked it down to
> some recent updates moving the internal utility labeledLine() from
> BiocGenerics to S4Vectors. The labeledLine() internal function wasn’t being
> found when called in certain circumstances. Here’s an svn diff to fix the
> bug in the S4Vectors package.
>
>
> Cheers,
>
> Pete
>
>
> Index: DESCRIPTION
>
> ===
>
> --- DESCRIPTION (revision 107278)
>
> +++ DESCRIPTION (working copy)
>
> @@ -8,7 +8,7 @@
>
> interest (e.g. DataFrame, Rle, and Hits) are implemented in the
>
> S4Vectors package itself (many more are implemented in the IRanges
>
> package and in other Bioconductor infrastructure packages).
>
> -Version: 0.7.12
>
> +Version: 0.7.13
>
> Author: H. Pages, M. Lawrence and P. Aboyoun
>
> Maintainer: Bioconductor Package Maintainer
>
> biocViews: Infrastructure, DataRepresentation
>
> Index: R/List-class.R
>
> ===
>
> --- R/List-class.R (revision 107278)
>
> +++ R/List-class.R (working copy)
>
> @@ -86,7 +86,7 @@
>
>cat(classNameForDisplay(object), " of length ", lo,
>
>"\n", sep = "")
>
>if (!is.null(names(object)))
>
> -cat(labeledLine("names", names(object)))
>
> +cat(S4Vectors:::labeledLine("names", names(object)))
>
>})
>
>
>
>
>
> Peter Hickey,
>
> PhD Student/Research Assistant,
>
> Bioinformatics Division,
>
> Walter and Eliza Hall Institute of Medical Research,
>
> 1G Royal Parade, Parkville, Vic 3052, Australia.
>
> Ph: +613 9345 2324
>
>
> hic...@wehi.edu.au
>
> http://www.wehi.edu.au
>
>
> __
>
> The information in this email is confidential and intended solely for the
> addressee.
>
> You must not disclose, forward, print or use it without the permission of
> the sender.
>
> __
>
>
>
> --
>
> Hervé Pagès
>
>
> Program in Computational Biology
>
> Division of Public Health Sciences
>
> Fred Hutchinson Cancer Research Center
>
> 1100 Fairview Ave. N, M1-B514
>
> P.O. Box 19024
>
> Seattle, WA 98109-1024
>
>
> E-mail: hpa...@fredhutch.org
>
> Phone: (206) 667-5791
>
> Fax:(206) 667-1319
>
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Re: [Bioc-devel] Missed change in S4Vectors
Hi Hervé,
Hmm, sorry I may have misdiagnosed my problem. I was having problems with
some code in the bsseq vignette.
The following demonstrates what was happening:
> suppressPackageStartupMessages(library(bsseq))
Warning message:
In .recacheSubclasses(def@className, def, doSubclasses, env) :
undefined subclass "externalRefMethod" of class "expressionORfunction";
definition not updated
> data(BS.chr22)
> head(seqnames(BS.chr22), n = 4)
factor-Rle of length 4 with 1 run
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'labeledLine' not found
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats4parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] bsseq_1.5.5SummarizedExperiment_0.3.3
[3] Biobase_2.29.1 GenomicRanges_1.21.18
[5] GenomeInfoDb_1.5.10IRanges_2.3.18
[7] S4Vectors_0.7.12 matrixStats_0.14.2
[9] BiocGenerics_0.15.6
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 Rcpp_0.12.0 lattice_0.20-33 gtools_3.5.0
[5] chron_2.3-47 plyr_1.8.3 grid_3.2.1 magrittr_1.5
[9] scales_0.2.5 stringi_0.5-5reshape2_1.4.1 XVector_0.9.1
[13] data.table_1.9.4 tools_3.2.1 stringr_1.0.0munsell_0.4.2
[17] colorspace_1.2-6
Once I made that proposed change to IRanges (locally) and re-install then
it works as expected.
Any ideas what I'm doing wrong?
Thanks,
Pete
Hi Peter,
Starting with S4Vectors 0.7.12, labeledLine() belongs to S4Vectors so
using the triple colon should not be necessary (and doing so will
actually trigger a note from R CMD check). Can you provide more
details on why you need this?
Thanks,
H.
On 08/09/2015 09:16 PM, Peter Hickey wrote:
Hi Hervé,
I was having trouble with some devel code of mine and tracked it down to
some recent updates moving the internal utility labeledLine() from
BiocGenerics to S4Vectors. The labeledLine() internal function wasn’t being
found when called in certain circumstances. Here’s an svn diff to fix the
bug in the S4Vectors package.
Cheers,
Pete
Index: DESCRIPTION
===
--- DESCRIPTION (revision 107278)
+++ DESCRIPTION (working copy)
@@ -8,7 +8,7 @@
interest (e.g. DataFrame, Rle, and Hits) are implemented in the
S4Vectors package itself (many more are implemented in the IRanges
package and in other Bioconductor infrastructure packages).
-Version: 0.7.12
+Version: 0.7.13
Author: H. Pages, M. Lawrence and P. Aboyoun
Maintainer: Bioconductor Package Maintainer
biocViews: Infrastructure, DataRepresentation
Index: R/List-class.R
===
--- R/List-class.R (revision 107278)
+++ R/List-class.R (working copy)
@@ -86,7 +86,7 @@
cat(classNameForDisplay(object), " of length ", lo,
"\n", sep = "")
if (!is.null(names(object)))
-cat(labeledLine("names", names(object)))
+cat(S4Vectors:::labeledLine("names", names(object)))
})
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324
hic...@wehi.edu.au
http://www.wehi.edu.au
__
The information in this email is confidential and intended solely for the
addressee.
You must not disclose, forward, print or use it without the permission of
the sender.
__
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Missed change in S4Vectors
Hi Peter,
Starting with S4Vectors 0.7.12, labeledLine() belongs to S4Vectors so
using the triple colon should not be necessary (and doing so will
actually trigger a note from R CMD check). Can you provide more
details on why you need this?
Thanks,
H.
On 08/09/2015 09:16 PM, Peter Hickey wrote:
Hi Hervé,
I was having trouble with some devel code of mine and tracked it down to some
recent updates moving the internal utility labeledLine() from BiocGenerics to
S4Vectors. The labeledLine() internal function wasn’t being found when called
in certain circumstances. Here’s an svn diff to fix the bug in the S4Vectors
package.
Cheers,
Pete
Index: DESCRIPTION
===
--- DESCRIPTION (revision 107278)
+++ DESCRIPTION (working copy)
@@ -8,7 +8,7 @@
interest (e.g. DataFrame, Rle, and Hits) are implemented in the
S4Vectors package itself (many more are implemented in the IRanges
package and in other Bioconductor infrastructure packages).
-Version: 0.7.12
+Version: 0.7.13
Author: H. Pages, M. Lawrence and P. Aboyoun
Maintainer: Bioconductor Package Maintainer
biocViews: Infrastructure, DataRepresentation
Index: R/List-class.R
===
--- R/List-class.R (revision 107278)
+++ R/List-class.R (working copy)
@@ -86,7 +86,7 @@
cat(classNameForDisplay(object), " of length ", lo,
"\n", sep = "")
if (!is.null(names(object)))
-cat(labeledLine("names", names(object)))
+cat(S4Vectors:::labeledLine("names", names(object)))
})
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324
hic...@wehi.edu.au
http://www.wehi.edu.au
__
The information in this email is confidential and inte...{{dropped:19}}
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