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

[Robert Castelo]

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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