Hello all,
I was hoping to use the devel version of my package "spoon" by installing
it with the devel version of BiocManager. I installed Bioconductor version
3.20 (BiocManager 1.30.23), R 4.4.0 (2024-04-24) and then tried
using BiocManager::install("spoon") to install the package. It installed
version 1.1.0, but I can see that 1.1.3 was built without errors at the
link below. Is there something else that must be done to allow 1.1.3 to be
installed?
https://bioconductor.org/checkResults/3.20/bioc-LATEST/spoon/
Please let me know if more information is needed, I haven't used the devel
branch before and am learning as I go!
Thank you,
Kinnary
> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
[1] TRUE
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.6.6
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;
LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] spoon_1.1.0
loaded via a namespace (and not attached):
[1] utf8_1.2.4 scuttle_1.15.0
[3] SparseArray_1.5.11 BiocVersion_3.20.0
[5] lattice_0.22-6 magrittr_2.0.3
[7] sparseMatrixStats_1.17.2 grid_4.4.0
[9] rprojroot_2.0.4 jsonlite_1.8.8
[11] Matrix_1.7-0 GenomeInfoDb_1.41.1
[13] limma_3.61.2 rdist_0.0.5
[15] BiocManager_1.30.23 httr_1.4.7
[17] fansi_1.0.6 SingleCellExperiment_1.27.2
[19] UCSC.utils_1.1.0 pbapply_1.7-2
[21] codetools_0.2-20 abind_1.4-5
[23] cli_3.6.3 rlang_1.1.4
[25] crayon_1.5.3 XVector_0.45.0
[27] Biobase_2.65.0 DelayedArray_0.31.3
[29] RANN_2.6.1 S4Arrays_1.5.2
[31] beachmat_2.21.3 tools_4.4.0
[33] parallel_4.4.0 BiocParallel_1.39.0
[35] SpatialExperiment_1.15.1 locfit_1.5-9.10
[37] GenomeInfoDbData_1.2.12 here_1.0.1
[39] SummarizedExperiment_1.35.1 BiocGenerics_0.51.0
[41] vctrs_0.6.5 R6_2.5.1
[43] magick_2.8.3 matrixStats_1.3.0
[45] stats4_4.4.0 lifecycle_1.0.4
[47] zlibbioc_1.51.1 S4Vectors_0.43.0
[49] edgeR_4.3.4 IRanges_2.39.0
[51] pkgconfig_2.0.3 pillar_1.9.0
[53] glue_1.7.0 Rcpp_1.0.12
[55] statmod_1.5.0 BRISC_1.0.5
[57] tibble_3.2.1 GenomicRanges_1.57.1
[59] rstudioapi_0.16.0 MatrixGenerics_1.17.0
[61] rjson_0.2.21 DelayedMatrixStats_1.27.1
[63] nnSVG_1.9.0 compiler_4.4.0
On Thu, Jun 13, 2024 at 2:15 PM Kinnary Shah <kinnarysh...@gmail.com> wrote:
> Thank you for the quick response, this is very helpful!
>
> On Thu, Jun 13, 2024 at 1:19 PM Kern, Lori <lori.sheph...@roswellpark.org>
> wrote:
>
>> A few things.
>>
>>
>> 1. Please keep in mind there is a delay from pushing to the
>> Bioconductor git and when it will be available via BiocManager. The
>> package must first get built and propagated on our system. The
>> checkResults page shows the timings of these reports currently twice a
>> week. https://bioconductor.org/checkResults/
>>
>> We hope to have devel builds back to daily builds soon.
>>
>>
>> 2. There are always two active branches of Bioconductor the release
>> and devel branches. If you push to default, which based on your
>> versioning
>> is where you pushed, this updates the devel branch only. You would also
>> need to push to RELEASE_3_19 to have changes visible on the release 3.19
>> branch. This versioning would be 1.0.0 to 1.0.1 as we generally keep
>> version_x.y.z of a package the y odd in devel and even in release.
>>
>>
>>
>> 3. As far as the ERROR from github install. You can check to see if
>> it also occurs on our build system once the builds pick up the pushed
>> devel
>> version but without digging into the code its hard to say if its used
>> properly or not. I will say that I just tried installing from github using
>> install_github and it seemed to install properly.
>>
>>
>> Hope this helps
>> Cheers!
>>
>>
>> Lori Shepherd - Kern
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> ------------------------------
>> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of
>> Kinnary Shah <kinnarysh...@gmail.com>
>> *Sent:* Thursday, June 13, 2024 1:04 PM
>> *To:* bioc-devel@r-project.org <bioc-devel@r-project.org>
>> *Subject:* [Bioc-devel] Package version did not update correctly
>>
>> Hello,
>>
>> I made some small changes to a function in my package, "spoon", and wanted
>> to update the patch version number to build the changes.
>>
>> https://secure-web.cisco.com/1zR5ERV81i3b1mbOVu4UUbWz7ccIbJzxw57R4EwygH5zgpfDlIjiFYWxi7jwY58iI-zQdwLnRqEcXoweBgmAu67NkxQi97-YNcDpGtjwvk7kaIAqVwU9gVCB9JRpfGKQOXijjUnkTN3lX3cE8T9S_DV1HGAgdWxNr4vcrKLeWPQPzUpSg5Bw_rlyH4lgCDBQIp8UJEyqQetzL8OKfdn9PDYDQDcwu6lk-AXuBB7hJCK060miWJYWvPeQ34yjGVK9eJhErf-u88mMHMNmEsye-Mf2HrErTKxlnVlsoRZ7u2_rpd1VTfOPPWD1gO9fGS7xJ/https%3A%2F%2Fgithub.com%2Fkinnaryshah%2Fspoon%2Ftree%2Fmain
>>
>> I updated the version from 1.1.0 to 1.1.1 and pushed the changes to the
>> Bioconductor and GitHub repositories. When I try to install through
>> BiocManager with Bioconductor 3.19, it installs 1.0.0. When I install
>> using
>> remotes to install from GitHub in R 4.4, it gives me the following error
>> and does not install:
>>
>> Error: Failed to install 'spoon' from GitHub:
>> $ operator is invalid for atomic vectors
>> In addition: Warning message:
>> In FUN(X[[i]], ...) :
>> DESCRIPTION file of package 'spoon' is missing or broken
>>
>> I have used the $ operator in the changes that I have made, but it is
>> valid
>> in the way that it has been used.
>>
>> I had to merge the DESCRIPTION file change before updating the version
>> number (
>> https://secure-web.cisco.com/1lj-E4tKIE1gqbIbd-TXxhNEHvtvREem72CgM4xPTwLEbxueLXtMO2TEQkWIqQmD6LH_P8NhVRk0fC0XSRyk9C1ipm1nAiWJQYLqzPxQRMG4fm6ucgkikMDwwloEcpALlul7LIFMV_OvebyuJjDpTIZpBUkqVzbaRu9bTdo9Me9j0KuhEJRtqv4wqRBwlk_qM-1kvlPZjFL4xfYAaLBvyEFTkKc-XQk5ikzbJP4Su-RBxxDAkqUB_2DehkzXc0zakmdWOoxq08cuIypiypxbxdEKAxaFKutmwrOSbh9VdFN-Udor2UU8czJd-3WxgLKkr/https%3A%2F%2Fgithub.com%2Fkinnaryshah%2Fspoon%2Fcommits%2Fmain%2F)
>> because I
>> incorrectly updated the version at first, so I'm not sure if this messed
>> up
>> the overall version updating.
>>
>> Please advise if more context is needed or if there are suggestions about
>> how to proceed.
>>
>> Thank you,
>> Kinnary
>>
>> [[alternative HTML version deleted]]
>>
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