[Bioc-devel] Package version did not update correctly
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 <kinnaryshahh at 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.Shepherd at 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-bounces at r-project.org> on behalf of Kinnary Shah <kinnaryshahh at gmail.com> *Sent:* Thursday, June 13, 2024 1:04 PM *To:* bioc-devel at r-project.org <bioc-devel at 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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