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

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 at 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 at 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 at r-project.org on behalf of 
robert.castelo at 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 at r-project.org mailing list
???? >????? >      
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???? >
???? >