I've fixed it and will push to R-devel as soon as it passes checks. Michael
On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrence <micha...@gene.com> wrote: > Just noticed this thread. I will look into this and hopefully fix it. > > On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: >> Hi, >> >> I made progress on this. This has actually nothing to do with Java. >> You get the same thing with the flexmix package. What rJava and flexmix >> have in common is that they both define a method on the base::unique() >> implicit S4 generic. >> >> The issue actually originates in the methods package. In order to remove >> rJava, BiocGenerics and IRanges from the equation, I made 2 minimalist >> packages, uniqueMethod and uniqueGeneric, that can be used to reproduce >> the issue. See: >> >> https://github.com/Bioconductor/uniqueGeneric >> >> I committed a workaround in S4Vectors (0.17.44). With this version of >> S4Vectors: >> >> library(rJava) >> library(IRanges) >> unique(IRanges()) >> # IRanges object with 0 ranges and 0 metadata columns: >> # start end width >> # <integer> <integer> <integer> >> >> Let me know if you still run into problems with this. >> >> Cheers, >> H. >> >>> sessionInfo() >> R Under development (unstable) (2018-02-26 r74306) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: Ubuntu 16.04.4 LTS >> >> Matrix products: default >> BLAS: /home/hpages/R/R-3.5.r74306/lib/libRblas.so >> LAPACK: /home/hpages/R/R-3.5.r74306/lib/libRlapack.so >> >> 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] stats4 parallel stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] IRanges_2.13.29 S4Vectors_0.17.44 BiocGenerics_0.25.3 >> [4] rJava_0.9-9 >> >> loaded via a namespace (and not attached): >> [1] compiler_3.5.0 >> >> >> On 04/14/2018 03:11 AM, Hervé Pagès wrote: >>> >>> Hi Zheng, >>> >>> I can totally reproduce this on my Ubuntu laptop: >>> >>> library(rJava) >>> library(IRanges) >>> unique(IRanges()) >>> # Error in validObject(.Object) : >>> # invalid class “MethodWithNext” object: Error : C stack usage >>> 7969396 is too close to the limit >>> >>> See my seesionInfo() at the end of this email. >>> >>> Probably related to this (but not 100% sure) loading rJava seems >>> to break selectMethod(). >>> >>> More precisely: The rJava package defines some "unique" S4 methods >>> and the BiocGenerics package defines (and exports) the unique() S4 >>> generic with the following statement: >>> >>> setGeneric("unique", signature="x") >>> >>> Here is what happens when loading the rJava package first: >>> >>> library(rJava) >>> library(BiocGenerics) >>> >>> setClass("A", slots=c(a="integer")) >>> setMethod("unique", "A", >>> function(x, incomparables=FALSE, ...) {x@a <- unique(x@a); x} >>> ) >>> >>> selectMethod("unique", "A") >>> # Method Definition (Class "derivedDefaultMethod"): >>> # >>> # function (x, incomparables = FALSE, ...) >>> # UseMethod("unique") >>> # <bytecode: 0x4127140> >>> # <environment: namespace:base> >>> # >>> # Signatures: >>> # x >>> # target "A" >>> # defined "ANY" >>> >>> selectMethod() doesn't find the method for A objects! >>> >>> It seems that selectMethod() is looking in the method table for >>> the implicit unique() generic defined in rJava instead of the >>> explicit unique() generic defined in BiocGenerics. If we tell >>> selectMethod() which generic to consider, then it finds the method >>> for A objects: >>> >>> selectMethod(BiocGenerics::unique, "A") >>> # Method Definition: >>> # >>> # function (x, incomparables = FALSE, ...) >>> # { >>> # x@a <- unique(x@a) >>> # x >>> # } >>> # >>> # Signatures: >>> # x >>> # target "A" >>> # defined "A" >>> >>> In order to reproduce the above problem without the BiocGenerics >>> package in the equation, it's not enough to do: >>> >>> library(rJava) >>> setGeneric("unique", signature="x") >>> etc... >>> >>> The setGeneric("unique", signature="x") statement must be put in >>> a package. I've created a minimalist package on GitHub that just >>> wraps this statement: >>> >>> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_uniqueGeneric&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=b4YM1TCcJjPge2siQJS5BQv7g1DMkoCQ-7FvZz89w-E&s=P9-WHLV4FmY9PQcNjkZ4Cgc24Oi1QTNVBqTaQ1iS-kg&e= >>> >>> This package can be used instead of BiocGenerics to reproduce the >>> problem above. >>> >>> I'm not 100% sure that this problem is related to the issue you >>> reported originally but it seems very likely to me. >>> >>> Not quite sure what the next step should be. I've been told by >>> some R core developers that there are known interaction issues >>> between Java, rJava and R that are currently being worked on. >>> Someone should ask on the R-devel mailing list or directly to >>> Simon Urbanek, the rJava author, for more information about this. >>> >>> H. >>> >>> > sessionInfo() >>> R Under development (unstable) (2018-02-26 r74306) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> Running under: Ubuntu 16.04.4 LTS >>> >>> Matrix products: default >>> BLAS: /home/hpages/R/R-3.5.r74306/lib/libRblas.so >>> LAPACK: /home/hpages/R/R-3.5.r74306/lib/libRlapack.so >>> >>> 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] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BiocGenerics_0.25.3 rJava_0.9-9 >>> >>> loaded via a namespace (and not attached): >>> [1] compiler_3.5.0 parallel_3.5.0 >>> >>> >>> On 04/02/2018 11:47 AM, Vincent Carey wrote: >>>> >>>> I get the following on MacOSX, after library(rJava); >>>> library(GenomicRanges) -- take rJava out of the mix and >>>> there is no error. I ran into this originally as an interaction between >>>> rJava and Gviz, and have reported to >>>> Florian. That seemed to be MacOSX-specific. >>>> >>>>> gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)), >>>> >>>> >>>> +ranges=IRanges(16:21, 20), >>>> >>>> +strand=rep(c("+", "-", "*"), 2)) >>>> >>>>> unique(gr1) >>>> >>>> >>>> *Error in validObject(.Object) :* >>>> >>>> *invalid class "MethodWithNext" object: Error : C stack usage7969864 is >>>> too close to the limit* >>>> >>>> *Error during wrapup: C stack usage7969656 is too close to the limit* >>>> >>>> * >>>> * >>>> >>>> ** >>>> >>>> *> sessionInfo()* >>>> >>>> * >>>> >>>> R Under development (unstable) (2018-02-14 r74250) >>>> >>>> Platform: x86_64-apple-darwin15.6.0 (64-bit) >>>> >>>> Running under: macOS Sierra 10.12.6 >>>> >>>> >>>> Matrix products: default >>>> >>>> BLAS: >>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.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] parallelstats4stats graphicsgrDevices utils datasets >>>> >>>> [8] methods base >>>> >>>> >>>> other attached packages: >>>> >>>> [1] GenomicRanges_1.31.23 GenomeInfoDb_1.15.5 IRanges_2.13.28 >>>> >>>> [4] S4Vectors_0.17.38 BiocGenerics_0.25.3 rJava_0.9-9 >>>> >>>> [7] rmarkdown_1.9 >>>> >>>> >>>> loaded via a namespace (and not attached): >>>> >>>> [1] Rcpp_0.12.16 digest_0.6.15rprojroot_1.3-2 >>>> >>>> [4] bitops_1.0-6 backports_1.1.2magrittr_1.5 >>>> >>>> [7] evaluate_0.10.1zlibbioc_1.25.0stringi_1.1.7 >>>> >>>> [10] XVector_0.19.9 tools_3.5.0stringr_1.3.0 >>>> >>>> [13] RCurl_1.95-4.10compiler_3.5.0 htmltools_0.3.6 >>>> >>>> [16] knitr_1.20 GenomeInfoDbData_1.1.0 >>>> >>>> >>>> * >>>> >>>> >>>> >>>> On Mon, Apr 2, 2018 at 2:25 PM, Hervé Pagès <hpa...@fredhutch.org >>>> <mailto:hpa...@fredhutch.org>> wrote: >>>> >>>> Hi Zheng, >>>> >>>> Thanks for the report. I will look into this and will let you know. >>>> >>>> H. >>>> >>>> On 04/01/2018 02:38 AM, Zheng Wei wrote: >>>> >>>> Dear all, >>>> >>>> I find this error if calling library(rJava) before using >>>> BiocGenerics::unique >>>> >>>> The code is pasted below. >>>> >>>> Thanks, >>>> Zheng >>>> >>>> > library(rJava) >>>> > library(GenomicRanges) >>>> Loading required package: stats4 >>>> Loading required package: BiocGenerics >>>> Loading required package: parallel >>>> >>>> Attaching package: ‘BiocGenerics’ >>>> >>>> The following objects are masked from ‘package:parallel’: >>>> >>>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ >>>> clusterExport, clusterMap, parApply, parCapply, parLapp >>>> parLapplyLB, parRapply, parSapply, parSapplyLB >>>> >>>> The following objects are masked from ‘package:rJava’: >>>> >>>> anyDuplicated, duplicated, sort, unique >>>> >>>> The following objects are masked from ‘package:stats’: >>>> >>>> IQR, mad, sd, var, xtabs >>>> >>>> The following objects are masked from ‘package:base’: >>>> >>>> anyDuplicated, append, as.data.frame, basename, cbind, >>>> colnames, colSums, dirname, do.call, duplicated, eval, >>>> Filter, Find, get, grep, grepl, intersect, is.unsorted, >>>> lengths, Map, mapply, match, mget, order, paste, pmax, >>>> pmin, pmin.int >>>> >>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pmin.int&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=WuplCAfYBn5Cq3N946mtZUi0612IchE0DfGaLDRFWTg&s=Km1Jhe0uxvMMuNveRSNtoTyFaOBZRO2jL8kmCFQd8Ec&e=>, >>>> Position, rank, rbind, Reduce, rowMeans >>>> rowSums, sapply, setdiff, sort, table, tapply, union, u >>>> unsplit, which, which.max, which.min >>>> >>>> Loading required package: S4Vectors >>>> >>>> >>>> Attaching package: ‘S4Vectors’ >>>> >>>> The following object is masked from ‘package:base’: >>>> >>>> expand.grid >>>> >>>> Loading required package: IRanges >>>> Loading required package: GenomeInfoDb >>>> > gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)), >>>> + ranges=IRanges(16:21, 20), >>>> + strand=rep(c("+", "-", "*"), 2)) >>>> > unique(gr1) >>>> Error: node stack overflow >>>> > BiocGenerics::unique(gr1) >>>> Error: node stack overflow >>>> >>>> >>>> >>>> -- 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 <mailto:hpa...@fredhutch.org> >>>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >>>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing >>>> list >>>> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=b4YM1TCcJjPge2siQJS5BQv7g1DMkoCQ-7FvZz89w-E&s=JNrsjIF-swIGjCJUiljVcp0KYi42-z3NNryBT3EZmSg&e= >>>> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=WuplCAfYBn5Cq3N946mtZUi0612IchE0DfGaLDRFWTg&s=Lw0PlsxUz2dbA2mDa_e4vZrNZ2FfjaNNQ-abMHuIMNY&e=> >>>> >>>> >>> >> >> -- >> 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 >> >> _______________________________________________ >> 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
