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.cast...@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.cast...@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-boun...@r-project.org on behalf of
robert.cast...@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]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> >
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