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 <kinnarysh...@gmail.com>
Sent: Wednesday, July 3, 2024 12:27 PM
To: Kern, Lori <lori.sheph...@roswellpark.org>
Cc: bioc-devel@r-project.org <bioc-devel@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
<kinnarysh...@gmail.com<mailto: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<mailto: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/<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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on
behalf of Kinnary Shah <kinnarysh...@gmail.com<mailto:kinnarysh...@gmail.com>>
Sent: Thursday, June 13, 2024 1:04 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
<bioc-devel@r-project.org<mailto: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
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