[Bioc-devel] Package version did not update correctly

Wed Jul 3 18:38:33 CEST 2024

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<mailto: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<mailto: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.

  1.
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.

  1.  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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Kinnary Shah <kinnaryshahh using gmail.com<mailto:kinnaryshahh using gmail.com>>
Sent: Thursday, June 13, 2024 1:04 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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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