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. 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 > _______________________________________________ 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