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 <st...@channing.harvard.edu>
Sent: 17 October 2018 16:14:56
To: Martin, Patrick C N
Cc: Shepherd, Lori; bioc-devel@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.mar...@essex.ac.uk<mailto:p.mar...@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.sheph...@roswellpark.org>
Sent: 17 October 2018 15:54:04
To: Martin, Patrick C N;
bioc-devel@r-project.org<mailto:bioc-devel@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This should indicate if there are any additional packages that are out-of-date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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on
behalf of Martin, Patrick C N
<p.mar...@essex.ac.uk<mailto:p.mar...@essex.ac.uk>>
Sent: Wednesday, October 17, 2018 10:40:34 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@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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