Bioconductor/BiocManager issues and pull requests

#197 - Typo fix

Pull Request - State: closed - Opened by almahmoud 22 days ago

#196 - Remove notion of biocLite.R. Closes #195

Pull Request - State: open - Opened by sneumann 4 months ago

#195 - Purge biocLite

Issue - State: open - Opened by sneumann 4 months ago

#194 - BiocManager::install() - Error in readRDS(dest) : error reading from connection

Issue - State: closed - Opened by HelenaLC 9 months ago - 6 comments

#193 - Force version of Bioconductor in use to env. variable R_BIOC_VERSION

Pull Request - State: closed - Opened by mtmorgan 10 months ago

#192 - add blurb regarding CRANhaven

Pull Request - State: closed - Opened by LiNk-NY 11 months ago

#191 - Fix Package Manager link in vignette

Pull Request - State: closed - Opened by bdeitte 11 months ago - 1 comment

#190 - IDEA: BiocManager::install() to fall back to CRANhaven for recently archived CRAN packages

Issue - State: open - Opened by HenrikBengtsson 12 months ago

#189 - Have install() fall back to CRANhaven except for Bioc devel

Pull Request - State: open - Opened by HenrikBengtsson 12 months ago

#188 - update use of package_version in unit tests

Pull Request - State: closed - Opened by mtmorgan 12 months ago

#187 - add default BioC_mirror for CI=TRUE env

Pull Request - State: open - Opened by LiNk-NY 12 months ago - 8 comments

#186 - Problem with BiocManager connection to Internet under Windows: problem solved

Issue - State: open - Opened by lokapal about 1 year ago - 5 comments

#185 - Using on Shiny and deploying on Posit

Issue - State: closed - Opened by natyfp about 1 year ago - 1 comment

#184 - use BiocStyle for the vignette

Pull Request - State: closed - Opened by LiNk-NY about 1 year ago

#183 - Version map cannot be validated - not mapping to new bioconductor website

Issue - State: open - Opened by aehrenberg over 1 year ago - 9 comments

#182 - add updating old packages section, closes #174

Pull Request - State: closed - Opened by LiNk-NY over 1 year ago

#181 - error in addGroupCoverages(ArchRProj = mp, groupBy = "Sample")

Issue - State: closed - Opened by yangchao4 over 1 year ago - 1 comment
Labels: invalid

#180 - Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), : Viewport has zero dimension(s)

Issue - State: closed - Opened by 15993561663 over 1 year ago - 2 comments

#179 - 'getOption("repos")' replaces Bioconductor standard repositories

Issue - State: closed - Opened by 15993561663 over 1 year ago - 1 comment

#178 - I can't download BiocManager but has been download

Issue - State: closed - Opened by 15993561663 over 1 year ago - 3 comments

#177 - version: Bioconductor version cannot be validated; no internet connection?

Issue - State: closed - Opened by 15993561663 over 1 year ago - 5 comments

#176 - ver.1.30.22: lazy-load database '/4.3.X_Rlib/BiocManager/R/BiocManager.rdb' is corrupt

Issue - State: closed - Opened by akhst7 over 1 year ago - 10 comments

#175 - Issue while using phyloseq with Bioconductor / SSL connect error

Issue - State: closed - Opened by sroblet over 1 year ago - 3 comments

#174 - Provide more guidance on what it means to 'update packages'

Issue - State: closed - Opened by mtmorgan over 1 year ago

#173 - include site_repository check in install and valid

Pull Request - State: closed - Opened by LiNk-NY over 1 year ago - 2 comments

#172 - filter BiocVersion from out_of_date matrix in .valid_result

Pull Request - State: closed - Opened by LiNk-NY over 1 year ago

#171 - Non zero exit status when installing mia package on M1

Issue - State: closed - Opened by emnatasha over 1 year ago - 2 comments

#170 - Allow site_repository env var or option

Pull Request - State: closed - Opened by LiNk-NY over 1 year ago

#169 - update docs to indicate purpose of offline use

Pull Request - State: closed - Opened by LiNk-NY over 1 year ago

#168 - Switching to BioC devel with 'BiocManager::install(version="devel")' installs BiocVersion twice

Issue - State: closed - Opened by hpages over 1 year ago

#167 - Update documentation

Pull Request - State: closed - Opened by mtmorgan over 1 year ago - 1 comment

#166 - use Bioc-devel branch on R-devel during the 'summer' release cycle

Pull Request - State: closed - Opened by mtmorgan over 1 year ago - 4 comments

#165 - Better document purpose of BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS

Issue - State: closed - Opened by mtmorgan almost 2 years ago

#164 - Provide exported function to determine BioC version for R version

Issue - State: open - Opened by hadley almost 2 years ago - 8 comments

#163 - Add site_repository environment variable and option

Pull Request - State: closed - Opened by LiNk-NY almost 2 years ago

#162 - site_repository not permanent

Issue - State: closed - Opened by LiNk-NY almost 2 years ago - 3 comments
Labels: enhancement, question

#161 - BiocManager does not respect `dependencies = TRUE` when the non-Suggests packages have already been installed

Issue - State: open - Opened by mtmorgan almost 2 years ago

#160 - man: \link in backtick blocks not supported by roxygen2

Pull Request - State: closed - Opened by aitap almost 2 years ago - 5 comments

#159 - packageVersion to return NA of class package_version

Pull Request - State: closed - Opened by LiNk-NY about 2 years ago - 5 comments

#158 - Local path install prompt not usable

Issue - State: closed - Opened by rbutleriii about 2 years ago - 3 comments

#157 - BiocManager::install(version = "devel", ask = FALSE) failing

Issue - State: closed - Opened by bbimber about 2 years ago - 3 comments

#156 - I can't run DECIPHER::IdClusters

Issue - State: closed - Opened by julietaalvarez about 2 years ago - 1 comment

#155 - Unable to use do_query() function

Issue - State: closed - Opened by digs1998 about 2 years ago - 1 comment

#154 - BiocManager::valid() does not check for 'missing' dependencies

Issue - State: open - Opened by mtmorgan about 2 years ago - 1 comment

#153 - BiocManager::install => no example of downloading specific package versions

Issue - State: closed - Opened by nick-youngblut about 2 years ago - 5 comments

#152 - clean up checkBuilt in lower levels

Pull Request - State: closed - Opened by LiNk-NY about 2 years ago

#151 - Rename cran repositories base

Pull Request - State: closed - Opened by LiNk-NY about 2 years ago - 3 comments

#150 - Clean up messages and docs

Pull Request - State: closed - Opened by LiNk-NY about 2 years ago

#149 - Repositories type arg

Pull Request - State: closed - Opened by LiNk-NY about 2 years ago

#148 - Installation problem in Bioconductor packages in R. BiocManager::intall() not working.

Issue - State: open - Opened by bakshiasif about 2 years ago - 3 comments

#147 - BiocManager::install() cannot install the package and displays an error

Issue - State: closed - Opened by Wangchao-98 about 2 years ago - 7 comments

#146 - BiocManager::install(version = "3.15", ask = FALSE, force = TRUE) error

Issue - State: closed - Opened by xec-cm about 2 years ago - 1 comment

#145 - BiocManager::install ignores type parameter

Issue - State: closed - Opened by jorainer over 2 years ago - 7 comments

#144 - WISH: Clarify "BiocManager.check_repositories" message and silence it in more cases?

Issue - State: open - Opened by HenrikBengtsson over 2 years ago - 1 comment

#143 - passing 'top level' arguments `checkBuilt`, `version`, `site_repository`

Issue - State: closed - Opened by LiNk-NY over 2 years ago

#142 - Error: argument "update" is missing, with no default

Issue - State: closed - Opened by grimbough over 2 years ago - 18 comments

#141 - catch zero length output from .version_map_config_element

Pull Request - State: closed - Opened by LiNk-NY over 2 years ago

#140 - Error: loading failed for install BiocManager packages

Issue - State: closed - Opened by zhoujiaqi704 over 2 years ago - 11 comments

#139 - BiocManager can't find mac ARM64 binaries

Issue - State: closed - Opened by jwokaty over 2 years ago - 4 comments
Labels: question

#138 - update warning / message when packages are too new

Pull Request - State: closed - Opened by LiNk-NY over 2 years ago

#137 - add update and ask arguments to .install_github and interpret

Pull Request - State: closed - Opened by LiNk-NY over 2 years ago

#136 - ask and update options does NOT work with BiocManager::install remotes package

Issue - State: closed - Opened by rgaiacs over 2 years ago - 2 comments

#135 - BiocManager::repositories() Reports Missing `books` for 3.15/3.16

Issue - State: open - Opened by jonyoder over 2 years ago - 9 comments

#134 - Install BiocManager successfully in R 4.2.1 but can't use on Windows

Issue - State: closed - Opened by gaospecial over 2 years ago - 2 comments

#133 - Default to Bioc devel for R-devel

Issue - State: closed - Opened by lshep over 2 years ago - 9 comments

#132 - Error: package or namespace load failed for ‘BiocManager’: .onAttach failed in attachNamespace() for 'BiocManager', details: call: if (max(r) == package_version("3.6")) { error: argument is of length zero

Issue - State: closed - Opened by Seraph-009 almost 3 years ago - 6 comments

#131 - test load fails on clean install of BiocManager

Issue - State: closed - Opened by LiNk-NY almost 3 years ago - 8 comments

#130 - Using R-devel when the version bumps before Bioconductor's version bumps?

Issue - State: closed - Opened by bbimber almost 3 years ago - 6 comments

#129 - argument force is missing with no default when upgrading from 3.13

Issue - State: closed - Opened by LiNk-NY about 3 years ago - 1 comment

#128 - BiocManager::install() not installing package if available version is lower than current

Issue - State: open - Opened by hpages about 3 years ago - 11 comments

#127 - pass `update` argument to `remotes::install_github`

Pull Request - State: closed - Opened by LiNk-NY about 3 years ago

#126 - Suppress the prompt from the remotes package

Issue - State: closed - Opened by Jiefei-Wang about 3 years ago - 1 comment

#125 - warning messages on windows

Issue - State: closed - Opened by LiNk-NY about 3 years ago - 2 comments

#124 - Suggested package BiocVersion cannot be installed during BiocManager installation

Issue - State: closed - Opened by pmoris about 3 years ago - 4 comments

#123 - get around NA values in map during offline use

Pull Request - State: closed - Opened by LiNk-NY about 3 years ago

#122 - BiocManager problems installing from local repository

Issue - State: closed - Opened by mtmorgan about 3 years ago - 4 comments

#121 - checking for already installed does not respect lib argument

Issue - State: open - Opened by lshep over 3 years ago - 4 comments

#120 - Option to restrict BiocManager::available() to Bioconductor packages

Issue - State: closed - Opened by kevinrue over 3 years ago - 6 comments

#119 - legacy version maps not available

Issue - State: closed - Opened by LiNk-NY over 3 years ago - 1 comment
Labels: enhancement

#118 - repos= not allowed if setting version?

Issue - State: closed - Opened by vjcitn over 3 years ago - 1 comment

#117 - BiocManager::install doesn't respect type argument

Issue - State: closed - Opened by jmacdon over 3 years ago - 3 comments

#116 - Add ENV var for binary package location

Pull Request - State: closed - Opened by LiNk-NY over 3 years ago - 7 comments

#115 - bugfix: re-convert warning to warning instead of character

Pull Request - State: closed - Opened by LiNk-NY over 3 years ago

#114 - Installing BiocManager corrupt .rdb file

Issue - State: closed - Opened by zpavlovi2703 over 3 years ago - 2 comments

#113 - Fixes for rmarkdown syntax errors in roxygen documentation code

Pull Request - State: closed - Opened by remlapmot over 3 years ago - 1 comment

#112 - Package not available warnings handled incorrectly

Issue - State: closed - Opened by mtmorgan over 3 years ago - 1 comment

#111 - Add Italian translation

Pull Request - State: closed - Opened by LiNk-NY over 3 years ago - 4 comments

#110 - Add Japanese translation

Pull Request - State: closed - Opened by kozo2 over 3 years ago

#109 - Added FR language support with changes from `sprintf` to `.msg`

Pull Request - State: closed - Opened by LiNk-NY over 3 years ago - 1 comment

#108 - Chinese translation

Pull Request - State: closed - Opened by Jiefei-Wang over 3 years ago

#107 - CI error on MacOS: argument "force" is missing, with no default

Issue - State: closed - Opened by ahmohamed over 3 years ago - 6 comments

#106 - Added the Spanish translation for some messages. Updated README-Translation.md

Pull Request - State: closed - Opened by rcastelo over 3 years ago - 5 comments

#105 - update the .install call in .install_updated_version

Pull Request - State: closed - Opened by LiNk-NY over 3 years ago - 1 comment

#104 - SingleCellExperiment load failed issue

Issue - State: closed - Opened by Lesdormis almost 4 years ago - 2 comments

#103 - installs binaries even when source is explicitly requested

Issue - State: closed - Opened by lshep almost 4 years ago - 7 comments

#102 - Disable R version checking on systems without internet connectivity

Issue - State: closed - Opened by jorainer almost 4 years ago - 7 comments

#101 - BiocManager ignores force=TRUE when installing from github

Issue - State: closed - Opened by lgeistlinger almost 4 years ago - 6 comments

GitHub / Bioconductor/BiocManager issues and pull requests