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

Fri Jun 5 17:28:10 CEST 2020

On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo <robert.castelo using upf.edu>
wrote:

> hi Vince,
>
> no worries, i've been finally able to reproduce the error in my computer
> and i'm afraid i'm probably using a deprecated dataset from 'gwascat',
> concretely the one that was stored as
>
> gwascat/data/ebicat37.rda
>
> what would be the replacement for the following kind of operation?
>

The best thing to do from a scientific point of view would likely be

curcat = gwascat::makeCurrentGwascat()

then work with that, which will have GRCh38 coordinates.

It is slow to run makeCurrentGwascat.  You might want to serialize what you
need.
I can't place a snapshot in gwascat as I had in the past because the image
compressed
with xz exceeds 5MB.  Any snapshot has to be in AnnotationHub.  I don't
have a
plan for this at the moment.

There is an object called ebicat_2020_04_30 in the data
folder of gwascat on devel branch.  It is a sample of 50000 records from
the full
catalog of that date.  You might be able to use that for what you are
doing; I will
be renaming it to clarify that it is a sample.

>
> data(ebicat37)
> eyersids <- unique(subsetByTraits(ebicat37, tr="Eye color")$SNPS)
> eyersids
>  [1] "rs12913832" "rs7173419"  "rs3002288"  "rs12896399" "rs1408799"
>  [6] "rs12520016" "rs288139"   "rs1667394"  "rs4596632"  "rs12203592"
> [11] "rs16891982" "rs1393350"  "rs1847134"
>
> thanks!
>
> robert.
>
> On 05/06/2020 14:06, Vincent Carey wrote:
>
> 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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