[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
Michael Lawrence
l@wrence@mich@el @ending from gene@com
Tue Nov 6 00:48:18 CET 2018
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.bioc using gmail.com>
wrote:
>
>
> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres" <
> bioc-devel-bounces using r-project.org on behalf of lcollado using 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 using 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 using 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 using 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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