Thank you for the info Martin and Michael! In the particular situation with recount and the xts warning, re-installing data.table 1.11.8 worked with xts 0.11.2. Details are further below.
Best, Leo On Mon, Nov 5, 2018 at 6:49 PM Michael Lawrence <lawrence.mich...@gene.com> wrote: > > For the general problem of understanding your package dependency structure, > see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html. Thanks for the link! > > > On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan <mtmorgan.b...@gmail.com> wrote: >> >> >> >> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres" >> <bioc-devel-boun...@r-project.org on behalf of lcoll...@jhu.edu> wrote: >> >> Hi bioc-devel, >> >> recount is getting a warning on Bioc 3.9 (devel) on macOS: >> >> * checking whether package ‘recount’ can be installed ... WARNING >> Found the following significant warnings: >> Warning: S3 method ‘xts::as.xts.data.table’ was declared in >> NAMESPACE but not found >> >> I'm not sure how to trace this since recount doesn't depend on xts. At >> least not directly. What is the best way to find which of the recount >> dependencies is triggering this NAMESPACE warning? While it's a >> warning in this case, it seems to break the installation of the GitHub >> package LieberInstitute/recount.bwtool as shown below. >> >> Can you reproduce this warning when you load recount in a new session? If >> so, you can >> >> options(warn = 2) # make them errors >> trace(registerS3methods, tracer = quote(print(package))) >> library(recount) Thanks, I didn't know about trace(regiserS3methods, tracer = quote(print(package))) ! And yes, I can reproduce the problem with this code. >> >> >> which will print out each package as it is loaded, the last being printed is >> the culprit. >> >> This failed a problem for me, but on the builder I see >> >> Tracing registerS3methods(nsInfo$S3methods, package, env) on entry >> [1] "data.table" >> Error: package or namespace load failed for ‘recount’: >> (converted from warning) S3 method ‘xts::as.xts.data.table’ was declared in >> NAMESPACE but not found >> >> The builder has >> >> > packageVersion("xts") >> [1] ‘0.11.1’ >> >> whereas I have 0.11.2. The reason is because my R installs xts from source >> where the most recent version is 0.11.2, whereas the builder plays like most >> mac users and installs built binaries. The last mac binary available is >> 0.11.1, as summarized here: >> >> https://cran.r-project.org/web/packages/xts/index.html >> >> where the Published date is 2018-11-05 (today!) and where the binaries are >> 0.11.1 but source is 0.11.2. Tracing registerS3methods(nsInfo$S3methods, package, env) on entry [1] "data.table" Error: package or namespace load failed for ‘recount’: (converted from warning) S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found > > packageVersion('xts') [1] ‘0.11.2’ > > sessionInfo() R Under development (unstable) (2018-11-02 r75540) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SummarizedExperiment_1.13.0 DelayedArray_0.9.0 [3] BiocParallel_1.17.0 matrixStats_0.54.0 [5] Biobase_2.43.0 GenomicRanges_1.35.0 [7] GenomeInfoDb_1.19.0 IRanges_2.17.0 [9] S4Vectors_0.21.0 BiocGenerics_0.29.1 [11] colorout_1.2-0 loaded via a namespace (and not attached): [1] bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2 [4] progress_1.2.0 httr_1.3.1 GenomicFiles_1.19.0 [7] tools_3.6.0 backports_1.1.2 R6_2.3.0 [10] rpart_4.1-13 DBI_1.0.0 lazyeval_0.2.1 [13] colorspace_1.3-2 nnet_7.3-12 tidyselect_0.2.5 [16] gridExtra_2.3 prettyunits_1.0.2 bit_1.1-14 [19] compiler_3.6.0 htmlTable_1.12 xml2_1.2.0 [22] rtracklayer_1.43.0 scales_1.0.0 checkmate_1.8.5 [25] readr_1.1.1 stringr_1.3.1 digest_0.6.18 [28] Rsamtools_1.35.0 foreign_0.8-71 GEOquery_2.51.0 [31] XVector_0.23.0 base64enc_0.1-3 pkgconfig_2.0.2 [34] htmltools_0.3.6 limma_3.39.1 BSgenome_1.51.0 [37] htmlwidgets_1.3 rlang_0.3.0.1 rstudioapi_0.8 [40] RSQLite_2.1.1 bindr_0.1.1 acepack_1.4.1 [43] dplyr_0.7.7 VariantAnnotation_1.29.0 RCurl_1.95-4.11 [46] magrittr_1.5 GenomeInfoDbData_1.2.0 Formula_1.2-3 [49] Matrix_1.2-15 Rcpp_0.12.19 munsell_0.5.0 [52] stringi_1.2.4 zlibbioc_1.29.0 plyr_1.8.4 [55] grid_3.6.0 blob_1.1.1 crayon_1.3.4 [58] lattice_0.20-38 Biostrings_2.51.0 splines_3.6.0 [61] GenomicFeatures_1.35.1 hms_0.4.2 knitr_1.20 [64] pillar_1.3.0 biomaRt_2.39.0 XML_3.98-1.16 [67] glue_1.3.0 latticeExtra_0.6-28 gtable_0.2.0 [70] purrr_0.2.5 tidyr_0.8.2 assertthat_0.2.0 [73] ggplot2_3.1.0 survival_2.43-1 tibble_1.4.2 [76] GenomicAlignments_1.19.0 AnnotationDbi_1.45.0 memoise_1.1.0 [79] bindrcpp_0.2.2 cluster_2.0.7-1 > >> >> >> A further complexity is that there are NO MAC BINARIES for R-devel so >> basically the build machine is stuck with this situation until the mac >> binaries become available... when binaries become available would be a >> question for the R-sig-mac mailing list, though likely it has been asked / >> answered there before... I re-installed data.table using the following ~/.R/Makevars and it all worked after that. CC=/usr/local/clang6/bin/clang OBJC=$CC F77=/usr/local/gfortran/bin/gfortran FC=$F77 CXX=/usr/local/clang6/bin/clang++ #LDFLAGS="-L/usr/local/clang6/lib -L/usr/local/lib" LDFLAGS=-L/usr/local/clang6/lib R_LD_LIBRARY_PATH=/usr/local/clang6/lib:/usr/local/lib DYLD_FALLBACK_LIBRARY_PATH=/usr/local/clang6/lib:/usr/local/lib ## I got to this ~/.R/Makevars in my quest to install rJava the other day https://github.com/s-u/rJava/issues/165#issuecomment-436046007 options(warn = 2) # make them errors trace(registerS3methods, tracer = quote(print(package))) library(recount) ## deleted output Tracing registerS3methods(nsInfo$S3methods, package, env) on entry [1] "recount" > > > packageVersion('data.table') [1] ‘1.11.8’ > sessionInfo() R Under development (unstable) (2018-11-02 r75540) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] recount_1.9.0 SummarizedExperiment_1.13.0 [3] DelayedArray_0.9.0 BiocParallel_1.17.0 [5] matrixStats_0.54.0 Biobase_2.43.0 [7] GenomicRanges_1.35.0 GenomeInfoDb_1.19.0 [9] IRanges_2.17.0 S4Vectors_0.21.0 [11] BiocGenerics_0.29.1 colorout_1.2-0 loaded via a namespace (and not attached): [1] bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2 [4] progress_1.2.0 httr_1.3.1 GenomicFiles_1.19.0 [7] doRNG_1.7.1 tools_3.6.0 backports_1.1.2 [10] R6_2.3.0 rpart_4.1-13 Hmisc_4.1-1 [13] DBI_1.0.0 lazyeval_0.2.1 colorspace_1.3-2 [16] nnet_7.3-12 withr_2.1.2 tidyselect_0.2.5 [19] gridExtra_2.3 prettyunits_1.0.2 bit_1.1-14 [22] compiler_3.6.0 htmlTable_1.12 derfinder_1.17.0 [25] xml2_1.2.0 pkgmaker_0.27 rtracklayer_1.43.0 [28] scales_1.0.0 checkmate_1.8.5 readr_1.1.1 [31] stringr_1.3.1 digest_0.6.18 Rsamtools_1.35.0 [34] foreign_0.8-71 rentrez_1.2.1 GEOquery_2.51.0 [37] XVector_0.23.0 base64enc_0.1-3 pkgconfig_2.0.2 [40] htmltools_0.3.6 bibtex_0.4.2 limma_3.39.1 [43] BSgenome_1.51.0 htmlwidgets_1.3 rlang_0.3.0.1 [46] rstudioapi_0.8 RSQLite_2.1.1 bindr_0.1.1 [49] jsonlite_1.5 acepack_1.4.1 dplyr_0.7.7 [52] VariantAnnotation_1.29.0 RCurl_1.95-4.11 magrittr_1.5 [55] GenomeInfoDbData_1.2.0 Formula_1.2-3 Matrix_1.2-15 [58] Rcpp_0.12.19 munsell_0.5.0 stringi_1.2.4 [61] zlibbioc_1.29.0 qvalue_2.15.0 bumphunter_1.25.0 [64] plyr_1.8.4 grid_3.6.0 blob_1.1.1 [67] crayon_1.3.4 lattice_0.20-38 Biostrings_2.51.0 [70] splines_3.6.0 GenomicFeatures_1.35.1 hms_0.4.2 [73] derfinderHelper_1.17.0 locfit_1.5-9.1 knitr_1.20 [76] pillar_1.3.0 rngtools_1.3.1 reshape2_1.4.3 [79] codetools_0.2-15 biomaRt_2.39.0 XML_3.98-1.16 [82] glue_1.3.0 downloader_0.4 latticeExtra_0.6-28 [85] data.table_1.11.8 foreach_1.4.4 gtable_0.2.0 [88] purrr_0.2.5 tidyr_0.8.2 assertthat_0.2.0 [91] ggplot2_3.1.0 xtable_1.8-3 survival_2.43-1 [94] tibble_1.4.2 iterators_1.0.10 registry_0.5 [97] GenomicAlignments_1.19.0 AnnotationDbi_1.45.0 memoise_1.1.0 [100] bindrcpp_0.2.2 cluster_2.0.7-1 > devtools::install_github('LieberInstitute/recount.bwtool') ## deleted output * installing *source* package ‘recount.bwtool’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Loading required package: colorout * DONE (recount.bwtool) > The warning is still present at https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html: I'll check again in a few days. >> >> >> Martin >> >> Anyhow, I might just wait a while as was recommended in another thread >> https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html. >> I'm assuming that there are no recount.bwtool R 3.6 macOS users :P >> Though it's worrisome if a package can't depend on recount right now >> on R 3.6 / Bioc 3.9. >> >> Thanks, >> Leo >> >> Main links: >> >> * >> https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html >> * https://github.com/leekgroup/recount >> * https://github.com/LieberInstitute/recount.bwtool >> >> Full info: >> >> > library('devtools') >> > install_github('LieberInstitute/recount.bwtool') >> Downloading GitHub repo LieberInstitute/recount.bwtool@master >> Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase, >> BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome, >> DelayedArray, derfinder, derfinderHelper, GenomeInfoDb, >> GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles, >> GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools, >> rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation, >> XVector, zlibbioc >> ✔ checking for file >> >> ‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’ >> (350ms) >> ─ preparing ‘recount.bwtool’: >> ✔ checking DESCRIPTION meta-information ... >> ─ checking for LF line-endings in source and make files and shell >> scripts >> ─ checking for empty or unneeded directories >> ─ building ‘recount.bwtool_0.99.29.tar.gz’ >> >> Loading required package: colorout >> * installing *source* package ‘recount.bwtool’ ... >> ** R >> ** inst >> ** byte-compile and prepare package for lazy loading >> Error: package or namespace load failed for ‘recount’: >> (converted from warning) S3 method ‘xts::as.xts.data.table’ was >> declared in NAMESPACE but not found >> Error : package ‘recount’ could not be loaded >> ERROR: lazy loading failed for package ‘recount.bwtool’ >> * removing >> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’ >> Error in i.p(...) : >> (converted from warning) installation of package >> >> ‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’ >> had non-zero exit status >> > traceback() >> 20: doWithOneRestart(return(expr), restart) >> 19: withOneRestart(expr, restarts[[1L]]) >> 18: withRestarts({ >> .Internal(.signalCondition(simpleWarning(msg, call), msg, >> call)) >> .Internal(.dfltWarn(msg, call)) >> }, muffleWarning = function() NULL) >> 17: .signalSimpleWarning("installation of package >> >> ‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’ >> had non-zero exit status", >> base::quote(i.p(...))) >> 16: warning(gettextf("installation of package %s had non-zero exit >> status", >> sQuote(update[i, 1L])), domain = NA) >> 15: i.p(...) >> 14: force(code) >> 13: force(code) >> 12: with_envvar(c(R_PROFILE_USER = temp_rprofile), { >> force(code) >> }) >> 11: with_rprofile_user("options(warn = 2)", i.p(...)) >> 10: force(code) >> 9: with_options(list(warn = 2), with_rprofile_user("options(warn = 2)", >> i.p(...))) >> 8: force(code) >> 7: with_envvar(c(R_LIBS = lib, R_LIBS_USER = lib, R_LIBS_SITE = lib), >> if (should_error_for_warnings()) { >> with_options(list(warn = 2), with_rprofile_user("options(warn >> = 2)", >> i.p(...))) >> } else { >> i.p(...) >> }) >> 6: safe_install_packages(pkgdir, repos = NULL, quiet = quiet, type = >> "source", >> ...) >> 5: install(source, dependencies = dependencies, upgrade = upgrade, >> force = force, quiet = quiet, build = build, build_opts = >> build_opts, >> repos = repos, type = type, ...) >> 4: FUN(X[[i]], ...) >> 3: vapply(remotes, install_remote, ..., FUN.VALUE = character(1)) >> 2: install_remotes(remotes, auth_token = auth_token, host = host, >> dependencies = dependencies, upgrade = upgrade, force = force, >> quiet = quiet, build = build, build_opts = build_opts, repos = >> repos, >> type = type, ...) >> 1: install_github("LieberInstitute/recount.bwtool") >> >> > library('recount') >> Warning message: >> S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not >> found >> >> > options(width = 120) >> > sessioninfo::session_info() >> ─ Session info >> ─────────────────────────────────────────────────────────────────────────────────────────────────────── >> setting value >> version R Under development (unstable) (2018-11-02 r75540) >> os macOS Mojave 10.14.1 >> system x86_64, darwin15.6.0 >> ui X11 >> language (EN) >> collate en_US.UTF-8 >> ctype en_US.UTF-8 >> tz America/New_York >> date 2018-11-05 >> >> ─ Packages >> ─────────────────────────────────────────────────────────────────────────────────────────────────────────── >> package * version date lib source >> acepack 1.4.1 2016-10-29 [1] CRAN (R 3.6.0) >> AnnotationDbi 1.45.0 2018-10-30 [1] Bioconductor >> assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.6.0) >> backports 1.1.2 2017-12-13 [1] CRAN (R 3.6.0) >> base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.6.0) >> bibtex 0.4.2 2017-06-30 [1] CRAN (R 3.6.0) >> bindr 0.1.1 2018-03-13 [1] CRAN (R 3.6.0) >> bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.6.0) >> Biobase * 2.43.0 2018-10-30 [1] Bioconductor >> BiocGenerics * 0.29.1 2018-11-01 [1] Bioconductor >> BiocParallel * 1.17.0 2018-10-30 [1] Bioconductor >> biomaRt 2.39.0 2018-10-30 [1] Bioconductor >> Biostrings 2.51.0 2018-10-30 [1] Bioconductor >> bit 1.1-14 2018-05-29 [1] CRAN (R 3.6.0) >> bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.0) >> bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0) >> blob 1.1.1 2018-03-25 [1] CRAN (R 3.6.0) >> BSgenome 1.51.0 2018-10-31 [1] Bioconductor >> bumphunter 1.25.0 2018-11-05 [1] Github >> (rafalab/bumphunter@6569fde) >> callr 3.0.0 2018-08-24 [1] CRAN (R 3.6.0) >> checkmate 1.8.5 2017-10-24 [1] CRAN (R 3.6.0) >> cli 1.0.1 2018-09-25 [1] CRAN (R 3.6.0) >> cluster 2.0.7-1 2018-04-13 [1] CRAN (R 3.6.0) >> codetools 0.2-15 2016-10-05 [1] CRAN (R 3.6.0) >> colorout * 1.2-0 2018-11-02 [1] Github >> (jalvesaq/colorout@cc5fbfa) >> colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.6.0) >> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) >> curl 3.2 2018-03-28 [1] CRAN (R 3.6.0) >> data.table 1.11.8 2018-09-30 [1] CRAN (R 3.6.0) >> DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.0) >> debugme 1.1.0 2017-10-22 [1] CRAN (R 3.6.0) >> DelayedArray * 0.9.0 2018-10-30 [1] Bioconductor >> derfinder 1.17.0 2018-10-30 [1] Bioconductor >> derfinderHelper 1.17.0 2018-10-30 [1] Bioconductor >> desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) >> devtools * 2.0.1 2018-10-26 [1] CRAN (R 3.6.0) >> digest 0.6.18 2018-10-10 [1] CRAN (R 3.6.0) >> doRNG 1.7.1 2018-06-22 [1] CRAN (R 3.6.0) >> downloader 0.4 2015-07-09 [1] CRAN (R 3.6.0) >> dplyr 0.7.7 2018-10-16 [1] CRAN (R 3.6.0) >> foreach 1.4.4 2017-12-12 [1] CRAN (R 3.6.0) >> foreign 0.8-71 2018-07-20 [1] CRAN (R 3.6.0) >> Formula 1.2-3 2018-05-03 [1] CRAN (R 3.6.0) >> fs 1.2.6 2018-08-23 [1] CRAN (R 3.6.0) >> GenomeInfoDb * 1.19.0 2018-10-30 [1] Bioconductor >> GenomeInfoDbData 1.2.0 2018-11-02 [1] Bioconductor >> GenomicAlignments 1.19.0 2018-10-30 [1] Bioconductor >> GenomicFeatures 1.35.1 2018-11-02 [1] Bioconductor >> GenomicFiles 1.19.0 2018-10-30 [1] Bioconductor >> GenomicRanges * 1.35.0 2018-10-30 [1] Bioconductor >> GEOquery 2.51.0 2018-10-30 [1] Bioconductor >> ggplot2 3.1.0 2018-10-25 [1] CRAN (R 3.6.0) >> glue 1.3.0 2018-07-17 [1] CRAN (R 3.6.0) >> gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0) >> gtable 0.2.0 2016-02-26 [1] CRAN (R 3.6.0) >> Hmisc 4.1-1 2018-01-03 [1] CRAN (R 3.6.0) >> hms 0.4.2 2018-03-10 [1] CRAN (R 3.6.0) >> htmlTable 1.12 2018-05-26 [1] CRAN (R 3.6.0) >> htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.0) >> htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.0) >> httr 1.3.1 2017-08-20 [1] CRAN (R 3.6.0) >> IRanges * 2.17.0 2018-10-30 [1] Bioconductor >> iterators 1.0.10 2018-07-13 [1] CRAN (R 3.6.0) >> jsonlite 1.5 2017-06-01 [1] CRAN (R 3.6.0) >> knitr 1.20 2018-02-20 [1] CRAN (R 3.6.0) >> lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.0) >> latticeExtra 0.6-28 2016-02-09 [1] CRAN (R 3.6.0) >> lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.6.0) >> limma 3.39.1 2018-11-01 [1] Bioconductor >> locfit 1.5-9.1 2013-04-20 [1] CRAN (R 3.6.0) >> magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) >> Matrix 1.2-15 2018-11-01 [1] CRAN (R 3.6.0) >> matrixStats * 0.54.0 2018-07-23 [1] CRAN (R 3.6.0) >> memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0) >> munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) >> nnet 7.3-12 2016-02-02 [1] CRAN (R 3.6.0) >> pillar 1.3.0 2018-07-14 [1] CRAN (R 3.6.0) >> pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.6.0) >> pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0) >> pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0) >> pkgmaker 0.27 2018-05-25 [1] CRAN (R 3.6.0) >> plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0) >> prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0) >> processx 3.2.0 2018-08-16 [1] CRAN (R 3.6.0) >> progress 1.2.0 2018-06-14 [1] CRAN (R 3.6.0) >> ps 1.2.0 2018-10-16 [1] CRAN (R 3.6.0) >> purrr 0.2.5 2018-05-29 [1] CRAN (R 3.6.0) >> qvalue 2.15.0 2018-10-30 [1] Bioconductor >> R6 2.3.0 2018-10-04 [1] CRAN (R 3.6.0) >> RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) >> Rcpp 0.12.19 2018-10-01 [1] CRAN (R 3.6.0) >> RCurl 1.95-4.11 2018-07-15 [1] CRAN (R 3.6.0) >> readr 1.1.1 2017-05-16 [1] CRAN (R 3.6.0) >> recount * 1.9.0 2018-10-30 [1] Bioconductor >> registry 0.5 2017-12-03 [1] CRAN (R 3.6.0) >> remotes 2.0.2 2018-10-30 [1] CRAN (R 3.6.0) >> rentrez 1.2.1 2018-03-05 [1] CRAN (R 3.6.0) >> reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) >> rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.6.0) >> rngtools 1.3.1 2018-05-15 [1] CRAN (R 3.6.0) >> rpart 4.1-13 2018-02-23 [1] CRAN (R 3.6.0) >> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) >> Rsamtools 1.35.0 2018-10-30 [1] Bioconductor >> RSQLite 2.1.1 2018-05-06 [1] CRAN (R 3.6.0) >> rstudioapi 0.8 2018-10-02 [1] CRAN (R 3.6.0) >> rtracklayer 1.43.0 2018-10-30 [1] Bioconductor >> S4Vectors * 0.21.0 2018-10-30 [1] Bioconductor >> scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.0) >> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) >> stringi 1.2.4 2018-07-20 [1] CRAN (R 3.6.0) >> stringr 1.3.1 2018-05-10 [1] CRAN (R 3.6.0) >> SummarizedExperiment * 1.13.0 2018-10-30 [1] Bioconductor >> survival 2.43-1 2018-11-03 [1] CRAN (R 3.6.0) >> testthat 2.0.1 2018-10-13 [1] CRAN (R 3.6.0) >> tibble 1.4.2 2018-01-22 [1] CRAN (R 3.6.0) >> tidyr 0.8.2 2018-10-28 [1] CRAN (R 3.6.0) >> tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0) >> usethis * 1.4.0 2018-08-14 [1] CRAN (R 3.6.0) >> VariantAnnotation 1.29.0 2018-10-30 [1] Bioconductor >> withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) >> XML 3.98-1.16 2018-08-19 [1] CRAN (R 3.6.0) >> xml2 1.2.0 2018-01-24 [1] CRAN (R 3.6.0) >> xtable 1.8-3 2018-08-29 [1] CRAN (R 3.6.0) >> XVector 0.23.0 2018-10-30 [1] Bioconductor >> zlibbioc 1.29.0 2018-10-30 [1] Bioconductor >> >> [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library >> > >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> 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