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

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Fri Jun 5 16:52:30 CEST 2020


no, the build system should only propagate packages that have passed build and check -- the goal is to make the life of the user easier and more reliable, us developers have to sweat the details!

Usually there is a single package that has changed and causes problems, and like in the present case a little detective work (once one knows what to look for) leads quickly to the suspect.

Martin

On 6/5/20, 10:18 AM, "Robert Castelo" <robert.castelo using upf.edu> wrote:

    Thanks Martin, i wasn't aware about that fact. i've cloned the gwascat 
    repo and been able to directly install from the directory and reproduce 
    the error. in this case, this was easy because it involved just one 
    package but with multiple broken package dependencies, i'd have to 
    manually clone each of them and install them to reproduce the error.

    would it be a good idea in the devel build system to propagate the tar 
    ball resulting of

    R CMD build --no-build-vignettes

    so that we get automatically updates for at least those whose problem is 
    in the vignettes only?

    robert.

    On 05/06/2020 15:37, Martin Morgan wrote:
    > 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
    >      >
    >      >
    >      >
    >      >      	[[alternative HTML version deleted]]
    >      >
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    >



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