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

Robert Castelo robert@c@@te|o @end|ng |rom up|@edu
Fri Jun 5 12:27:03 CEST 2020


my package GenomicScores is not building, see:


apparently, it is breaking in the following lines of its vignette:


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.


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

  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=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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