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Question: no method for coercing S4 class to a vector
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3.1 years ago by
Guest User12k
Guest User12k wrote:
Dear all, I have a similar problem to this poster here: http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for-coercing- this-s4-class-to-a-vector The error message is: Error in as.vector(x) : no method for coercing this S4 class to a vector In my case, however, I'm using the as.data.frame function on a GRanges object. When I source my function it works fine, but when I make it into a package and then run the function I get the S4 class error. The function seems to be from BiocGenerics: > as.data.frame standardGeneric for "as.data.frame" defined from package "BiocGenerics" function (x, row.names = NULL, optional = FALSE, ...) standardGeneric("as.data.frame") <environment: 0x3801ad8=""> Methods may be defined for arguments: x Use showMethods("as.data.frame") for currently available ones. So, I have included this importFrom("BiocGenerics", as.data.frame) in NAMESPACE and this Depends: BiocGenerics in DESCRIPTION. It still does not work. I must be missing something. Any help is highly appreciated! Thanks Ninni -- output of sessionInfo(): > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-pc-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=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rtracklayer_1.24.0 GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 [4] IRanges_1.22.10 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 [4] Biostrings_2.32.0 bitops_1.0-6 brew_1.0-6 [7] BSgenome_1.32.0 codetools_0.2-9 DBI_0.2-7 [10] digest_0.6.4 fail_1.2 foreach_1.4.2 [13] GenomicAlignments_1.0.0 iterators_1.0.7 plyr_1.8.1 [16] Rcpp_0.11.1 RCurl_1.95-4.1 Rsamtools_1.16.0 [19] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.1 [22] stringr_0.6.2 tools_3.1.1 XML_3.98-1.1 [25] XVector_0.4.0 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 3.1 years ago by Andrzej Oleś670 • written 3.1 years ago by Guest User12k
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gravatar for Andrzej Oleś
3.1 years ago by
Andrzej Oleś670
EMBL Heidelberg, Germany
Andrzej Oleś670 wrote:
Dear Ninni, you probably need to import the 'as.data.frame' method for GRanges objects in your NAMESPACE file: importMethodsFrom(GenomicRanges, as.data.frame) Cheers, Andrzej On Fri, Sep 12, 2014 at 10:27 AM, Ninni Nahm [guest] <guest at="" bioconductor.org=""> wrote: > > Dear all, > > I have a similar problem to this poster here: > > http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for- coercing-this-s4-class-to-a-vector > > The error message is: > > Error in as.vector(x) : no method for coercing this S4 class to a vector > > > In my case, however, I'm using the as.data.frame function on a GRanges object. When I source my function it works fine, but when I make it into a package and then run the function I get the S4 class error. > > The function seems to be from BiocGenerics: > >> as.data.frame > standardGeneric for "as.data.frame" defined from package "BiocGenerics" > > function (x, row.names = NULL, optional = FALSE, ...) > standardGeneric("as.data.frame") > <environment: 0x3801ad8=""> > Methods may be defined for arguments: x > Use showMethods("as.data.frame") for currently available ones. > > > So, I have included this > importFrom("BiocGenerics", as.data.frame) > in NAMESPACE > > and this > Depends: BiocGenerics > in DESCRIPTION. > > It still does not work. I must be missing something. > > Any help is highly appreciated! > > Thanks > Ninni > > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.1.1 (2014-07-10) > Platform: x86_64-pc-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=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] rtracklayer_1.24.0 GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 > [4] IRanges_1.22.10 BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 > [4] Biostrings_2.32.0 bitops_1.0-6 brew_1.0-6 > [7] BSgenome_1.32.0 codetools_0.2-9 DBI_0.2-7 > [10] digest_0.6.4 fail_1.2 foreach_1.4.2 > [13] GenomicAlignments_1.0.0 iterators_1.0.7 plyr_1.8.1 > [16] Rcpp_0.11.1 RCurl_1.95-4.1 Rsamtools_1.16.0 > [19] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.1 > [22] stringr_0.6.2 tools_3.1.1 XML_3.98-1.1 > [25] XVector_0.4.0 zlibbioc_1.10.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 3.1 years ago by Andrzej Oleś670
Thank you! That did the trick! On Fri, Sep 12, 2014 at 2:45 PM, Andrzej Ole? <andrzej.oles at="" gmail.com=""> wrote: > Dear Ninni, > > you probably need to import the 'as.data.frame' method for GRanges > objects in your NAMESPACE file: > > importMethodsFrom(GenomicRanges, as.data.frame) > > > Cheers, > Andrzej > > On Fri, Sep 12, 2014 at 10:27 AM, Ninni Nahm [guest] > <guest at="" bioconductor.org=""> wrote: > > > > Dear all, > > > > I have a similar problem to this poster here: > > > > > http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for- coercing-this-s4-class-to-a-vector > > > > The error message is: > > > > Error in as.vector(x) : no method for coercing this S4 class to a vector > > > > > > In my case, however, I'm using the as.data.frame function on a GRanges > object. When I source my function it works fine, but when I make it into a > package and then run the function I get the S4 class error. > > > > The function seems to be from BiocGenerics: > > > >> as.data.frame > > standardGeneric for "as.data.frame" defined from package "BiocGenerics" > > > > function (x, row.names = NULL, optional = FALSE, ...) > > standardGeneric("as.data.frame") > > <environment: 0x3801ad8=""> > > Methods may be defined for arguments: x > > Use showMethods("as.data.frame") for currently available ones. > > > > > > So, I have included this > > importFrom("BiocGenerics", as.data.frame) > > in NAMESPACE > > > > and this > > Depends: BiocGenerics > > in DESCRIPTION. > > > > It still does not work. I must be missing something. > > > > Any help is highly appreciated! > > > > Thanks > > Ninni > > > > > > -- output of sessionInfo(): > > > >> sessionInfo() > > R version 3.1.1 (2014-07-10) > > Platform: x86_64-pc-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=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] rtracklayer_1.24.0 GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 > > [4] IRanges_1.22.10 BiocGenerics_0.10.0 > > > > loaded via a namespace (and not attached): > > [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 > > [4] Biostrings_2.32.0 bitops_1.0-6 brew_1.0-6 > > [7] BSgenome_1.32.0 codetools_0.2-9 DBI_0.2-7 > > [10] digest_0.6.4 fail_1.2 foreach_1.4.2 > > [13] GenomicAlignments_1.0.0 iterators_1.0.7 plyr_1.8.1 > > [16] Rcpp_0.11.1 RCurl_1.95-4.1 Rsamtools_1.16.0 > > [19] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.1 > > [22] stringr_0.6.2 tools_3.1.1 XML_3.98-1.1 > > [25] XVector_0.4.0 zlibbioc_1.10.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 3.1 years ago by Ninni Nahm50
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