[Bioc-devel] Unable to reproduce chimeraviz 3.10 build failure
Shepherd, Lori
Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Fri Oct 18 14:38:25 CEST 2019
The build system has the following R check environment variables active
_R_CHECK_LENGTH_1_CONDITION_ =package:_R_CHECK_PACKAGE_NAME_
_R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_
So the conditional lengths greater than one are treated as ERROR not WARNINGS.
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Stian L�gstad <stianlagstad using gmail.com>
Sent: Thursday, October 17, 2019 3:18 PM
To: Pages, Herve <hpages using fredhutch.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Unable to reproduce chimeraviz 3.10 build failure
Thank you for the help. I'm still unable to reproduce the error. I'm
working from the docker image bioconductor/devel_core2 (the latest version
at the time of writing). Opening the R session I see this:
```
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Bioconductor version 3.10 (BiocManager 1.30.4), ?BiocManager::install for
help
```
After loading chimeraviz, this is my sessionInfo():
```
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
datasets
[9] methods base
other attached packages:
[1] chimeraviz_1.11.0 testthat_2.2.1 data.table_1.12.2
[4] ensembldb_2.9.6 AnnotationFilter_1.9.0 GenomicFeatures_1.37.4
[7] AnnotationDbi_1.47.1 Biobase_2.45.1 Gviz_1.29.1
[10] GenomicRanges_1.37.16 GenomeInfoDb_1.21.1 Biostrings_2.53.2
[13] XVector_0.25.0 IRanges_2.19.16 S4Vectors_0.23.25
[16] BiocGenerics_0.31.5 BiocManager_1.30.4
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 ellipsis_0.2.0.1
[3] rprojroot_1.3-2 biovizBase_1.33.1
[5] htmlTable_1.13.1 ArgumentCheck_0.10.2
[7] base64enc_0.1-3 fs_1.3.1
[9] dichromat_2.0-0 rstudioapi_0.10
[11] roxygen2_6.1.1 remotes_2.1.0
[13] DT_0.9 bit64_0.9-7
[15] xml2_1.2.2 splines_3.6.1
[17] knitr_1.25 pkgload_1.0.2
[19] zeallot_0.1.0 Formula_1.2-3
[21] Rsamtools_2.1.5 cluster_2.1.0
[23] dbplyr_1.4.2 graph_1.63.0
[25] compiler_3.6.1 httr_1.4.1
[27] backports_1.1.4 assertthat_0.2.1
[29] Matrix_1.2-17 lazyeval_0.2.2
[31] cli_1.1.0 org.Mm.eg.db_3.8.2
[33] acepack_1.4.1 htmltools_0.3.6
[35] prettyunits_1.0.2 tools_3.6.1
[37] gtable_0.3.0 glue_1.3.1
[39] GenomeInfoDbData_1.2.1 dplyr_0.8.3
[41] rappdirs_0.3.1 Rcpp_1.0.2
[43] xopen_1.0.0 vctrs_0.2.0
[45] rtracklayer_1.45.6 xfun_0.9
[47] stringr_1.4.0 ps_1.3.0
[49] gtools_3.8.1 devtools_2.2.0
[51] XML_3.98-1.20 org.Hs.eg.db_3.8.2
[53] zlibbioc_1.31.0 RCircos_1.2.1
[55] scales_1.0.0 BiocStyle_2.13.2
[57] BSgenome_1.53.2 VariantAnnotation_1.31.4
[59] clisymbols_1.2.0 hms_0.5.1
[61] ProtGenerics_1.17.4 SummarizedExperiment_1.15.9
[63] RColorBrewer_1.1-2 yaml_2.2.0
[65] curl_4.1 memoise_1.1.0
[67] gridExtra_2.3 ggplot2_3.2.1
[69] rcmdcheck_1.3.3 biomaRt_2.41.8
[71] rpart_4.1-15 latticeExtra_0.6-28
[73] stringi_1.4.3 RSQLite_2.1.2
[75] desc_1.2.0 checkmate_1.9.4
[77] pkgbuild_1.0.5 BiocParallel_1.19.2
[79] commonmark_1.7 rlang_0.4.0
[81] pkgconfig_2.0.2 matrixStats_0.55.0
[83] bitops_1.0-6 evaluate_0.14
[85] lattice_0.20-38 purrr_0.3.2
[87] GenomicAlignments_1.21.7 htmlwidgets_1.3
[89] bit_1.1-14 processx_3.4.1
[91] tidyselect_0.2.5 plyr_1.8.4
[93] magrittr_1.5 R6_2.4.0
[95] Hmisc_4.2-0 DelayedArray_0.11.4
[97] DBI_1.0.0 pillar_1.4.2
[99] foreign_0.8-72 withr_2.1.2
[101] survival_2.44-1.1 RCurl_1.95-4.12
[103] nnet_7.3-12 tibble_2.1.3
[105] crayon_1.3.4 BiocFileCache_1.9.1
[107] rmarkdown_1.15 progress_1.2.2
[109] usethis_1.5.1 Rgraphviz_2.29.0
[111] blob_1.2.0 callr_3.3.1
[113] digest_0.6.20 openssl_1.4.1
[115] munsell_0.5.0 sessioninfo_1.1.1
[117] askpass_1.1
```
When running these lines (from your email):
```
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)
```
I get this output:
```
Fetching transcripts for gene partners..
..transcripts fetched.
Selecting transcripts for RCC1..
..found transcripts of type exonBoundary
Selecting transcripts for HENMT1..
..found transcripts of type exonBoundary
Warning messages:
1: In if (!any(start(transcripts_upstream) < fusion using gene_upstream@breakpoint)
& :
the condition has length > 1 and only the first element will be used
2: In if (!any(start(transcripts_downstream) <
fusion using gene_downstream@breakpoint)
& :
the condition has length > 1 and only the first element will be used
```
and the expected plot. I do see the warnings there, but I don't get an
error.
Any pointers would be very welcome. Thanks again.
On Wed, Oct 2, 2019 at 10:29 PM Pages, Herve <hpages using fredhutch.org> wrote:
> 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 L�gstad 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
> > ```
> >
>
> --
> Herv� Pag�s
>
> 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: hpages using fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
Stian L�gstad
+47 41 80 80 25
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