[Bioc-devel] GenomicScores: irreproducible build error caused by gwascat
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Tue Jun 9 04:20:26 CEST 2020
On 6/5/20 07:52, Martin Morgan wrote:
> no, the build system should only propagate packages that have passed build and check -- the goal is to make the life of the user easier and more reliable, us developers have to sweat the details!
This makes a lot of sense for release but for devel maybe the criteria
for propagating a package could be relaxed? It doesn't sound too insane
to do that but I realize it does introduce a difference between release
and devel that could also cause its own confusion.
Another approach that is currently under consideration is to make
BiocManager::install() capable of installing/updating packages directly
from git.bioconductor.org in BioC devel. This could be achieved by
making the source tarballs resulting from
git checkout master https://git.bioconductor.org/packages/<pkg> &&
R CMD build --no-build-vignettes <pkg>
available in their own repo (e.g.
https://bioconductor.org/packages/devel) and add this repo to
BiocManager::repositories() in devel. Note that these no-vignettes
source tarballs are actually those used by the build system during the
INSTALL stage.
How do people feel about that?
H.
>
> Usually there is a single package that has changed and causes problems, and like in the present case a little detective work (once one knows what to look for) leads quickly to the suspect.
>
> Martin
>
> On 6/5/20, 10:18 AM, "Robert Castelo" <robert.castelo using upf.edu> wrote:
>
> Thanks Martin, i wasn't aware about that fact. i've cloned the gwascat
> repo and been able to directly install from the directory and reproduce
> the error. in this case, this was easy because it involved just one
> package but with multiple broken package dependencies, i'd have to
> manually clone each of them and install them to reproduce the error.
>
> would it be a good idea in the devel build system to propagate the tar
> ball resulting of
>
> R CMD build --no-build-vignettes
>
> so that we get automatically updates for at least those whose problem is
> in the vignettes only?
>
> robert.
>
> On 05/06/2020 15:37, Martin Morgan wrote:
> > R CMD INSTALL <foo> or install.packages("foo", repos = NULL) on a clone of the repository. A build might fail because the examples or vignette fail to build, whereas for installation the only requirement is that the package is syntactically correct.
> >
> > Martin
> >
> > On 6/5/20, 7:58 AM, "Robert Castelo" <robert.castelo using upf.edu> wrote:
> >
> > never thought about it this way, but how can the system install
> > something that does not build?
> >
> > how should *i* install something that does not build to reproduce the error?
> >
> > sorry if these are very naive questions!!
> >
> > robert.
> >
> > On 05/06/2020 13:34, Martin Morgan wrote:
> > > The build system installs the version of gwascat that is available from git checkout (anticipating that this will propagate). gwascat installs, but fails to pass check -- it is likely broken
> > >
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_gwascat_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uJnw6vW_sTWKb9l6DPFY7NEqPq_zkEzDFbIrir-Xis8&s=r_GJJMDdjgc6nXTDSC0OhJW6gho041eSiWwKrw3h00w&e=
> > >
> > > in a way that causes your package to fail
> > >
> > > Martin
> > >
> > > On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" <bioc-devel-bounces using r-project.org on behalf of robert.castelo using upf.edu> wrote:
> > >
> > > hi,
> > >
> > > my package GenomicScores is not building, see:
> > >
> > > https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_GenomicScores_malbec1-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uJnw6vW_sTWKb9l6DPFY7NEqPq_zkEzDFbIrir-Xis8&s=-TxA290vxOPuMjHcxETokMk-jPL8H_YJpKMIr3UL50E&e=
> > >
> > > 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
> > >
> > >
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
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> >
>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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