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

[Vincent Carey]

I am really sorry about the situation with gwascat and will try to
straighten it out today.

On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo <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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