I just pushed it to the 3.5 branch. On Mon, Apr 30, 2018 at 2:14 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Excellent! Are you planning to commit this to the 3.5 branch too? > In that case we'll wait a couple more days before installing R 3.5 > patched on the build machines for the BioC 3.8 builds. > > Thanks, > H. > > > On 04/30/2018 01:43 PM, Michael Lawrence wrote: >> >> It's checked into devel now. Thanks for the well documented examples, >> Hervé. >> >> On Mon, Apr 30, 2018 at 10:26 AM, Michael Lawrence <micha...@gene.com> >> wrote: >>> >>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_uniqueGeneric&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=hI6LWw_u7csv2YoouDZz4PmV3GnTtE0movmB_pZuog8&s=5UWyuXnFrW3P7eeuT0jq8O9gi7BOreYKUmZ0LdDpJ3M&e= >>>>> >>>>> >>>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=hI6LWw_u7csv2YoouDZz4PmV3GnTtE0movmB_pZuog8&s=NJsCdpN9A1bsrpPUJSfAS8wTz1sXycGRPlBKr4-2M0E&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 >
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