[Bioc-devel] BioC 3.8 build Error

[Vincent Carey]

I also attempted to replicate and I found that one of your serialized data
elements (eveLocus)
was a GRanges that needed updateObject

However I would like to raise a question about this:

if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){

    if (!requireNamespace("BiocManager", quietly=TRUE))

        install.packages("BiocManager")

    BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")

    }

library(BSgenome.Dmelanogaster.UCSC.dm3)


I think that installing packages in vignettes should be

avoided.  You can put BSgenome.Dmelanogaster.UCSC.dm3 in

Suggests.


On Wed, Oct 17, 2018 at 11:12 AM, Martin, Patrick C N <p.martin using essex.ac.uk>
wrote:

> Hi Lori,
>
>
> Thank you very much! That seemed to have done the trick. At least now I
> can replicate the error.
>
>
> Thank you for your help.
>
>
>
> Kind Regards
>
>
>
> Patrick Martin
>
> ________________________________
> From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> Sent: 17 October 2018 15:54:04
> To: Martin, Patrick C N; bioc-devel using r-project.org
> Subject: Re: BioC 3.8 build Error
>
>
> I am able to reproduce this ERROR on a local copy of the ChIPanalyser
>  cloned from git.bioconductor.org  (version 1.3.5)
>
>
>
> Please make sure all package and associated package are updated.
> BiocInstaller is being deprecated so I suggest using BiocManager to update
> the packages
>
>
>
> install.packages("BiocManager")
>
> library(BiocManager)
>
> install(version="3.8")
>
> This should indicate if there are any additional packages that are
> out-of-date
>
>
>
> From the looks of your sessionInfo  you have a mixture of release and
> devel versions of packages so the above should suggest which packages need
> to be updated.  Once you update all versions of the packages, please see if
> you can replicate the ERROR.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Martin,
> Patrick C N <p.martin using essex.ac.uk>
> Sent: Wednesday, October 17, 2018 10:40:34 AM
> To: bioc-devel using r-project.org
> Subject: [Bioc-devel] BioC 3.8 build Error
>
> To whom it may concern,
>
>
> It has recently come to my attention that my package ( ChIPanalyser1.3.2
> on BioC 3.8) generates a build error.
>
>
> However, I cannot seem to replicate that error on my local machine. The
> version of the package that I have pushed towards both github
> (patrickCNMartin/ChIPanalyser) and to bioconductor passes both R CMD build
> and R CMD check on my local machine.
>
>
> I suspected that my R version could be outdated ( I was running R3.4.1)
> however even after updating to R3.5.1 and updating all relevant packages, I
> still cannot replicate the error. ChIPanalyser still passes through Build
> and Check.
>
>
> I also tested ChIPanalyser1.3.1 that is available on the devel branch to
> see if that one would build on my local machine and it does (also passes R
> CMD check ).
>
>
> Here is my sessionInfo()
>
>
> R version 3.5.1 (2018-07-02)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.1 LTS
>
> Matrix products: default
> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] GenomicRanges_1.32.7 GenomeInfoDb_1.16.0  IRanges_2.14.12
> [4] S4Vectors_0.18.3     BiocGenerics_0.26.0  BiocInstaller_1.30.0
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.26.0        compiler_3.5.1         XVector_0.20.0
> [4] tools_3.5.1            GenomeInfoDbData_1.1.0 RCurl_1.95-4.11
> [7] bitops_1.0-6
>
>
>
> I am currently out of ideas on how to replicate and fix the build error.
>
>
> Thank you for your help.
>
>
>
> Kind Regards
>
>
>
>
> Patrick Martin
>
>
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