[Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Martin Morgan]

R CMD INSTALL <foo> or install.packages("foo", repos = NULL) on a clone of the repository. A build might fail because the examples or vignette fail to build, whereas for installation the only requirement is that the package is syntactically correct.

Martin

On 6/5/20, 7:58 AM, "Robert Castelo" <robert.castelo using upf.edu> wrote:

    never thought about it this way, but how can the system install 
    something that does not build?

    how should *i* install something that does not build to reproduce the error?

    sorry if these are very naive questions!!

    robert.

    On 05/06/2020 13:34, Martin Morgan wrote:
    > The build system installs the version of gwascat that is available from git checkout (anticipating that this will propagate). gwascat installs, but fails to pass check -- it is likely broken
    >
    >    https://bioconductor.org/checkResults/devel/bioc-LATEST/gwascat/
    >
    > in a way that causes your package to fail
    >
    > Martin
    >
    > On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" <bioc-devel-bounces using r-project.org on behalf of robert.castelo using upf.edu> wrote:
    >
    >      hi,
    >
    >      my package GenomicScores is not building, see:
    >
    >      http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
    >
    >      apparently, it is breaking in the following lines of its vignette:
    >
    >      library(gwascat)
    >      data(ebicat37)
    >
    >      which in the report from the bioc build machine says:
    >
    >      gwascat loaded.  Use makeCurrentGwascat() to extract current image.
    >        from EBI.  The data folder of this package has some legacy extracts.
    >      Quitting from lines 404-408 (GenomicScores.Rmd)
    >      Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
    >      object 'ebicat37' not found
    >      --- failed re-building ‘GenomicScores.Rmd’
    >
    >      however, in my installation of current bioc-devel on R-4.0 with all
    >      packages up to date, GenomicScores builds fine and i cannot reproduce
    >      this error. below you can find my session information after the previous
    >      two instructions. the logs of 'gwascat' show changes in May 2nd that
    >      could be potentially responsible for this but the fact is that 'gwascat'
    >      is not building either and it does not seem that the changes propagate
    >      through the build system, its version is still 2.21.0, on which
    >      GenomicScores built without problems for the current release.
    >
    >      i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case he
    >      has some more specific suggestion about this but any hint will be
    >      greatly appreciated.
    >
    >      thanks!!
    >
    >      sessionInfo()
    >      R version 4.0.0 (2020-04-24)
    >      Platform: x86_64-pc-linux-gnu (64-bit)
    >      Running under: CentOS Linux 7 (Core)
    >
    >      Matrix products: default
    >      BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
    >      LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
    >
    >      locale:
    >        [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
    >        [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
    >        [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
    >        [7] LC_PAPER=en_US.UTF8       LC_NAME=C
    >        [9] LC_ADDRESS=C              LC_TELEPHONE=C
    >      [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
    >
    >      attached base packages:
    >      [1] stats     graphics  grDevices utils     datasets methods   base
    >
    >      other attached packages:
    >      [1] gwascat_2.21.0 colorout_1.2-2
    >
    >      loaded via a namespace (and not attached):
    >        [1] Rcpp_1.0.4.6 lattice_0.20-41
    >        [3] prettyunits_1.1.1 Rsamtools_2.5.1
    >        [5] Biostrings_2.57.1 assertthat_0.2.1
    >        [7] digest_0.6.25 BiocFileCache_1.13.0
    >        [9] R6_2.4.1 GenomeInfoDb_1.25.1
    >      [11] stats4_4.0.0 RSQLite_2.2.0
    >      [13] httr_1.4.1 ggplot2_3.3.1
    >      [15] pillar_1.4.4 zlibbioc_1.35.0
    >      [17] rlang_0.4.6 GenomicFeatures_1.41.0
    >      [19] progress_1.2.2 curl_4.3
    >      [21] blob_1.2.1 S4Vectors_0.27.11
    >      [23] Matrix_1.2-18 BiocParallel_1.23.0
    >      [25] stringr_1.4.0 RCurl_1.98-1.2
    >      [27] bit_1.1-15.2 biomaRt_2.45.0
    >      [29] munsell_0.5.0 DelayedArray_0.15.1
    >      [31] compiler_4.0.0 rtracklayer_1.49.3
    >      [33] pkgconfig_2.0.3 askpass_1.1
    >      [35] BiocGenerics_0.35.3 openssl_1.4.1
    >      [37] tidyselect_1.1.0 SummarizedExperiment_1.19.4
    >      [39] tibble_3.0.1 GenomeInfoDbData_1.2.3
    >      [41] IRanges_2.23.7 matrixStats_0.56.0
    >      [43] XML_3.99-0.3 crayon_1.3.4
    >      [45] dplyr_1.0.0 dbplyr_1.4.4
    >      [47] GenomicAlignments_1.25.1 bitops_1.0-6
    >      [49] rappdirs_0.3.1 grid_4.0.0
    >      [51] gtable_0.3.0 lifecycle_0.2.0
    >      [53] DBI_1.1.0 magrittr_1.5
    >      [55] scales_1.1.1 stringi_1.4.6
    >      [57] XVector_0.29.1 ellipsis_0.3.1
    >      [59] generics_0.0.2 vctrs_0.3.0
    >      [61] tools_4.0.0 bit64_0.9-7
    >      [63] Biobase_2.49.0 glue_1.4.1
    >      [65] purrr_0.3.4 hms_0.5.3
    >      [67] parallel_4.0.0 colorspace_1.4-1
    >      [69] AnnotationDbi_1.51.0 GenomicRanges_1.41.3
    >      [71] memoise_1.1.0
    >
    >
    >
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