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-boun...@r-project.org on behalf of robert.cast...@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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
