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

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 at r-project.org on behalf of robert.castelo at 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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