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.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 > > > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
