[Bioc-devel] BioC 3.8 build Error

[Martin, Patrick C N]

Hi Vincent,


Thank you for your suggestion. I will remove that part in the vignette and solve the build error with both of suggestions.



Kind Regards




Patrick

________________________________
From: Vincent Carey <stvjc using channing.harvard.edu>
Sent: 17 October 2018 16:14:56
To: Martin, Patrick C N
Cc: Shepherd, Lori; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] BioC 3.8 build Error

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<mailto: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<mailto: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<http://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This should indicate if there are any additional packages that are out-of-date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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Martin, Patrick C N <p.martin using essex.ac.uk<mailto:p.martin using essex.ac.uk>>
Sent: Wednesday, October 17, 2018 10:40:34 AM
To: bioc-devel using r-project.org<mailto: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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