[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

Martin Morgan mtmorg@n@bioc @ending from gm@il@com
Tue Nov 6 00:41:06 CET 2018



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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