Hi Stian,
The 3.10 builds use BioC 3.10 which is the current **devel** version of
BioC so make sure you also use this if you want to reproduce a 3.10
build failure.
Here is how to quickly reproduce the error:
library(chimeraviz)
defuse833ke <- system.file(
"extdata",
"defuse_833ke_results.filtered.tsv",
package="chimeraviz")
fusions <- import_defuse(defuse833ke, "hg19", 1)
fusion <- get_fusion_by_id(fusions, 5267)
edbSqliteFile <- system.file(
"extdata",
"Homo_sapiens.GRCh37.74.sqlite",
package="chimeraviz")
edb <- ensembldb::EnsDb(edbSqliteFile)
fusion5267and11759reads <- system.file(
"extdata",
"fusion5267and11759reads.bam",
package="chimeraviz")
plot_fusion_transcript(
fusion,
edb,
fusion5267and11759reads)
# Error in normarg_mcols(value, class(x), length(x)) :
# trying to set zero length metadata columns on a non-zero length
object
See my sessionInfo() below.
Anyway, this error is actually caused by a regression I introduced
recently to the S4Vectors package. Should be fixed now (in S4Vectors
0.23.25). Some details here:
https://github.com/Bioconductor/S4Vectors/commit/e53a50d4003b0d45aee69779998fcfb76a685690
If everything goes as expected, the build error in chimeraviz should go
away on tomorrow's report.
Sorry for the inconvenience,
H.
> sessionInfo()
R version 3.6.0 Patched (2019-05-02 r76454)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.6.r76454/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.6.r76454/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] chimeraviz_1.11.0 data.table_1.12.2 ensembldb_2.9.6
[4] AnnotationFilter_1.9.0 GenomicFeatures_1.37.4 AnnotationDbi_1.47.1
[7] Biobase_2.45.1 Gviz_1.29.3 GenomicRanges_1.37.16
[10] GenomeInfoDb_1.21.2 Biostrings_2.53.2 XVector_0.25.0
[13] IRanges_2.19.16 S4Vectors_0.23.24 BiocGenerics_0.31.6
loaded via a namespace (and not attached):
[1] ProtGenerics_1.17.4 bitops_1.0-6
[3] matrixStats_0.55.0 bit64_0.9-7
[5] RColorBrewer_1.1-2 progress_1.2.2
[7] httr_1.4.1 tools_3.6.0
[9] backports_1.1.4 DT_0.9
[11] R6_2.4.0 rpart_4.1-15
[13] Hmisc_4.2-0 DBI_1.0.0
[15] lazyeval_0.2.2 colorspace_1.4-1
[17] nnet_7.3-12 tidyselect_0.2.5
[19] gridExtra_2.3 prettyunits_1.0.2
[21] bit_1.1-14 curl_4.2
[23] compiler_3.6.0 htmlTable_1.13.2
[25] DelayedArray_0.11.6 rtracklayer_1.45.6
[27] scales_1.0.0 checkmate_1.9.4
[29] askpass_1.1 RCircos_1.2.1
[31] rappdirs_0.3.1 stringr_1.4.0
[33] digest_0.6.21 Rsamtools_2.1.6
[35] foreign_0.8-72 rmarkdown_1.16
[37] base64enc_0.1-3 dichromat_2.0-0
[39] pkgconfig_2.0.3 htmltools_0.3.6
[41] dbplyr_1.4.2 BSgenome_1.53.2
[43] htmlwidgets_1.3 rlang_0.4.0
[45] rstudioapi_0.10 RSQLite_2.1.2
[47] BiocParallel_1.19.3 acepack_1.4.1
[49] dplyr_0.8.3 VariantAnnotation_1.31.4
[51] RCurl_1.95-4.12 magrittr_1.5
[53] GenomeInfoDbData_1.2.1 Formula_1.2-3
[55] Matrix_1.2-17 Rcpp_1.0.2
[57] munsell_0.5.0 yaml_2.2.0
[59] stringi_1.4.3 SummarizedExperiment_1.15.9
[61] zlibbioc_1.31.0 plyr_1.8.4
[63] org.Hs.eg.db_3.8.2 BiocFileCache_1.9.1
[65] blob_1.2.0 crayon_1.3.4
[67] lattice_0.20-38 splines_3.6.0
[69] hms_0.5.1 zeallot_0.1.0
[71] knitr_1.25 pillar_1.4.2
[73] biomaRt_2.41.8 XML_3.98-1.20
[75] glue_1.3.1 evaluate_0.14
[77] biovizBase_1.33.1 latticeExtra_0.6-28
[79] BiocManager_1.30.4 vctrs_0.2.0
[81] org.Mm.eg.db_3.8.2 gtable_0.3.0
[83] openssl_1.4.1 purrr_0.3.2
[85] assertthat_0.2.1 ggplot2_3.2.1
[87] xfun_0.10 ArgumentCheck_0.10.2
[89] survival_2.44-1.1 tibble_2.1.3
[91] GenomicAlignments_1.21.7 memoise_1.1.0
[93] cluster_2.1.0 BiocStyle_2.13.2
On 10/2/19 11:27, Stian Lågstad wrote:
> Hi,
>
> The most recent build of chimeraviz fails when rebuilding the vignette:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_chimeraviz_malbec1-2Dbuildsrc.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UJ6fJMh-a_gWEyrhxw-8R4NRmxLgBEwS5BAsWho6xEU&s=AJDC2yvC23fZff7t5a-pwOsxPLZZJVMo614bEkL5lHY&e=
> ,
> and I'm unable to reproduce this locally. Does anyone have ideas as to how
> I can dig deeper into this?
>
> Thank you.
>
> Here's an excerpt from build log in case it disappears when the new build
> is done:
> ```
> Quitting from lines 564-591 (chimeraviz-vignette.Rmd)
> Error: processing vignette 'chimeraviz-vignette.Rmd' failed with
> diagnostics:
> trying to set zero length metadata columns on a non-zero length
> object
> --- failed re-building ‘chimeraviz-vignette.Rmd’
>
> SUMMARY: processing the following file failed:
> ‘chimeraviz-vignette.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
> ```
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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