[Bioc-devel] Package version did not update correctly

Wed Jul 3 19:00:40 CEST 2024

Thank you so much!

On Wed, Jul 3, 2024 at 12:38 PM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> It looks like this 1.1.3 version was just pushed and built today.  It will
> propagate today per the green radio button on the report.  I imagine if you
> try again in an hour or so that version will be available.  There is a
> little delay from the report to the propagation.
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Kinnary Shah <kinnaryshahh using gmail.com>
> *Sent:* Wednesday, July 3, 2024 12:27 PM
> *To:* Kern, Lori <Lori.Shepherd using RoswellPark.org>
> *Cc:* bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject:* Re: [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/
> <https://secure-web.cisco.com/1z48OczOXgJWETvyPygUCQc5Xyn6DpXOQdx-8cP3dm20g3AH3KWRNGn0Y4mkvoY2tN8UO-P2WIzmjogHFoDyWxJ-5Nxu0poOPsGtZM7gKLRZWgFa4vayND-HV2RcIebgGFL1yvr_ZffzO-0GYzx54u1duLDxoECzsFD4O1OTpRAEtn2-Gd8Fp3jmAvBPmmTgA82VzjIUjyDoG0BOKDFmXNQb2GMLX9CRCoRpVrWlWJ_v7UW-RMJSk7k102c8ewot6t6x7EylWyaZ21n4hhcmAbBFbzF-ebm4P_EWaBZrAzh8f8npnJiz8XojNVhmiQ_cX/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.20%2Fbioc-LATEST%2Fspoon%2F>
>
> 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/
> <https://secure-web.cisco.com/1MHxsLMmrpvA4duF0SGv-j6_b-1x0ncJXhrJFJMJ_RbXARYChkvS0lTFPjUqjiZqTcuCoxoOOOj0vHeHEqU6S5Ea29_3mXuAjH5xPlsqx4JIYlLUnuX9kjl1P0WWqVhW6YT6a0I9Eu2Cpykhroy4nHWtM7nyDzLNUm2QjpHkauB1xxTJSb4WIZ5RV_f_IIqOuOEJWLPLO_xmEDvgXqHUjphadhUTZfqi3weE5-Ilk3HrFkm8rKloe4DBjSCyGlHm1b3tFfi-RL6-MoJCS9zNCaNYu3DLj-YC0k_RRx7xponli5rwQ8PDZUKf_tP7ErQo1/https%3A%2F%2Fcran.rstudio.com%2F>
> [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 using 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 using 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/
>    <https://secure-web.cisco.com/1crOl_MCZIKURU8kLUfG_igimrV2O818LGcYtxMCPPyAoF4UA7mKrh05G_fypNVB5g5mwfQnjlhnAuzjqaSF8p7bUApDnMRkIjvgcsjd2fzPwix_7NGuwKfiRhcpGfAvIk7jRX4_NJ4T5ejpvWE7NNY2D5sc0f5iuB6czPzrWriv16afJsurASmgkCO6olxw8za81y5f18-flk8zMyFGqWvz0afEV7kmRx7CDqvftBrwQ48ouHWw4YvRYDwLQxcPAP8LiWH8dzp9lJAW9Z5Ujw8ynt85X96u17JtnKT4cF8h8wdoZ_syg25nMxDJyEubh/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F>
>
> 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 using r-project.org> on behalf of
> Kinnary Shah <kinnaryshahh using gmail.com>
> *Sent:* Thursday, June 13, 2024 1:04 PM
> *To:* bioc-devel using r-project.org <bioc-devel using 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
>
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>
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