'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 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/
<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 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]]