For the general problem of understanding your package dependency structure, see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html.
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) > > 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. > > 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... > > 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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel