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GitHub / Bioconductor/BiocParallel issues and pull requests

#278 - convert Rnw vignettes to Rmd

Pull Request - State: open - Opened by LiNk-NY 2 months ago

#276 - DoparParam: Disable capturing of stdout?

Issue - State: open - Opened by HenrikBengtsson 2 months ago

#275 - accuracy of doc on bpexportvariables

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

#274 - memory efficient parallel compting

Issue - State: open - Opened by ArthurPERE 4 months ago - 4 comments

#273 - Installation Failure

Issue - State: open - Opened by Fred-White94 4 months ago - 1 comment

#272 - frequent "Page not found" error for source package

Issue - State: closed - Opened by gbdias 4 months ago - 5 comments

#271 - Patch boost library issue

Issue - State: closed - Opened by mtmorgan 4 months ago

#269 - Allow user-provided NULL value in bplapply

Pull Request - State: closed - Opened by Jiefei-Wang 4 months ago

#268 - Use do.call() instead of lapply() in `bpoptions` (addressing issue #266)

Pull Request - State: closed - Opened by csoneson 6 months ago - 1 comment

#267 - bplapply does not handle NULL values

Issue - State: closed - Opened by RonanDaly 6 months ago - 2 comments

#266 - Can't find `bpprogressbar` unless `BiocParallel` is in `Depends`

Issue - State: closed - Opened by csoneson 6 months ago - 2 comments

#264 - Installation problem

Issue - State: closed - Opened by coralzhang 7 months ago - 3 comments

#263 - bplist_error does not report the error element index

Issue - State: closed - Opened by ChangqingW 9 months ago - 4 comments

#262 - S4 method for `[` not found in SNOW parallel processes

Issue - State: closed - Opened by jorainer 10 months ago - 1 comment

#261 - BiocParallel errors: first remote error: Error in model.frame.default

Issue - State: closed - Opened by TPlatek 11 months ago - 9 comments

#260 - strategy of tasks in MulticoreParam

Issue - State: closed - Opened by z5ouyang over 1 year ago - 4 comments

#259 - BiocParallel socketConnection error

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

#258 - Extremely minor: typo in docs? man/MulticoreParam-class.Rd

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

#257 - BatchtoolsParam fails to propagate errors in bpiterate

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

#256 - BiocParallel for parallelization in BEER: Error and GPU Compatibility

Issue - State: closed - Opened by FarzanehRah about 2 years ago - 8 comments

#255 - BiocParallel : long vectors are not supported in .C()

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

#254 - I meet a error when I use BiocParallel

Issue - State: closed - Opened by fadedmeliodas about 2 years ago - 6 comments

#253 - remove static messages no longer used by bplapply

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

#252 - BiocParallel errors：could not find function ".OLD_read_block"

Issue - State: closed - Opened by alopehba about 2 years ago - 11 comments

#250 - move Rmpi to Enhances:

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

#249 - Handle worker abort better

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

#248 - BiocParallel errors

Issue - State: closed - Opened by psjyot over 2 years ago - 4 comments

#247 - The running time isn't reduced when using bplapply()?

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

#246 - improve traceback in remote errors

Pull Request - State: closed - Opened by mtmorgan over 2 years ago - 2 comments

#244 - start TransientMulticoreParam, ensuring clean-up of environments

Pull Request - State: closed - Opened by mtmorgan over 2 years ago - 3 comments

#243 - MulticoreParam bplapply unable to restart upon interrupt

Issue - State: closed - Opened by gdagstn over 2 years ago - 1 comment

#242 - Force evaluation of the function argument

Pull Request - State: closed - Opened by Jiefei-Wang over 2 years ago - 2 comments

#241 - Troubles with bplapply within function (using SnowParam on Windows)

Issue - State: closed - Opened by DavoSam over 2 years ago - 6 comments

#240 - stop.on.error = FALSE for DoParam doesn't work as expected

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

#239 - Nested parallellization question

Issue - State: closed - Opened by zeehio over 2 years ago - 6 comments

#238 - Performance (speed) degradation in MulticoreParam with default force.G = TRUE

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

#237 - Error in serialize(data, node$con, xdr = FALSE) : ignoring SIGPIPE signal

Issue - State: closed - Opened by nickhsmith over 2 years ago - 5 comments

#236 - update configure.ac to use C++

Pull Request - State: closed - Opened by mtmorgan over 2 years ago - 3 comments

#235 - Fix issue 234

Pull Request - State: closed - Opened by Jiefei-Wang over 2 years ago - 2 comments

#234 - exported entities are destroyed in caller

Issue - State: closed - Opened by vjcitn over 2 years ago - 4 comments

#233 - [low-importance] [one-line] Add ORCID identifier

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

#232 - `bpnworkers(SnowParam(x))` is not integer

Issue - State: closed - Opened by LTLA over 2 years ago

#231 - WISH: Support also SnowParam(type = "PSOCK")

Issue - State: open - Opened by HenrikBengtsson over 2 years ago - 4 comments

#229 - Let environment variables override `workers = ` argument

Issue - State: closed - Opened by mtmorgan almost 3 years ago - 7 comments

#227 - Fix bpmapply performance

Pull Request - State: closed - Opened by zeehio almost 3 years ago

#226 - @Bioconductor/sweave2rmd: Conversion of Introduction_to_BiocParallel.Rnw to Rmd

Pull Request - State: closed - Opened by phyleria almost 3 years ago - 8 comments

#225 - Converting Introduction to BiocParallel.rnw to R Markdown

Issue - State: closed - Opened by phyleria almost 3 years ago - 4 comments

#224 - Exclude the internal object when exporting variables from the master

Pull Request - State: closed - Opened by Jiefei-Wang almost 3 years ago - 1 comment

#223 - Error using conflicted with BiocParallel in R4.2.0

Issue - State: closed - Opened by hxin almost 3 years ago - 7 comments

#222 - Template file for Slurm job submission

Issue - State: closed - Opened by mitmurakami almost 3 years ago - 1 comment

#221 - Errors_Logs_And_Debugging Rnw to Rmd

Pull Request - State: closed - Opened by villafup almost 3 years ago - 2 comments

#220 - g++ Error installing BiocParallel

Issue - State: closed - Opened by lmansilla26 almost 3 years ago - 2 comments

#219 - Biocparallel batchtoolsparam rmd

Pull Request - State: closed - Opened by villafup almost 3 years ago - 2 comments

#218 - Updates to vignette and function documentation

Pull Request - State: closed - Opened by DarioS almost 3 years ago

#217 - For Developers Vignette Section Lacks a Code Example

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

#216 - BiocParallel doesn't propagate warnings

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

#215 - Random_Numbers to Rmd

Pull Request - State: closed - Opened by mcarlsn about 3 years ago - 4 comments

#214 - 'offset' contains negative indices

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

#213 - ERROR: compilation failed for package 'BiocParallel'/g++: command not found

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

#212 - Make 'codetools' a required package?

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

#211 - Add the load balancer for evenly distributing the tasks across workers

Pull Request - State: open - Opened by Jiefei-Wang about 3 years ago - 11 comments

#209 - Improve the readability of the unit test result

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

#208 - Having issue with installing the BiocParallel

Issue - State: closed - Opened by DrSunYi about 3 years ago - 6 comments

#206 - wrong args for environment subassignment

Issue - State: closed - Opened by wanlinrong about 3 years ago - 5 comments

#205 - Deprecate BatchJobsParam

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

#204 - Reset the RNG seed stream when the RNG seed is reset

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

#203 - Rewrite DoparParam using the manager interface

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

#202 - update C++ code using cpp11

Pull Request - State: closed - Opened by Jiefei-Wang over 3 years ago - 7 comments

#201 - Do not include the flag -lrt on windows

Pull Request - State: closed - Opened by Jiefei-Wang over 3 years ago - 2 comments

#200 - BiocParallel too strict on type of `options(timeout)`

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

#199 - Suppress the startup message from the package in the worker

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

#198 - 'automatic' package attach on workers generates noisy startup messages

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

#197 - Add ... to .manager_send

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

#196 - Add Rstudio files to .gitignore and .Rbuildignore

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

#195 - Add Rstudio files to .gitignore and .Rbuildignore

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

#194 - fix a minor print issue in error handling function

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

#193 - timeout & bpoptions

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

#191 - [patch 2] bpfallback

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

#190 - [patch 1] Add 'bpoptions'

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

#189 - BioParallel errors: first remote error: cannot open the connection

Issue - State: closed - Opened by MuyaoXi9271 over 3 years ago - 3 comments

#188 - allow the user to pass an infinite task number

Pull Request - State: closed - Opened by Jiefei-Wang over 3 years ago - 2 comments

#187 - Check the port status before creating the cluster

Pull Request - State: closed - Opened by Jiefei-Wang over 3 years ago - 6 comments

#186 - allow SnowParam to work with devtools

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

#184 - allow automatically exporting the global variables used in the function

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

#183 - Do not export the global environment for the SerialParam

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

#182 - Add task cache feature and enable it by default for the SnowParam

Pull Request - State: closed - Opened by Jiefei-Wang over 3 years ago - 2 comments

#181 - fix a validation issue for BiocParallelParam

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

#180 - implement the task cache for the SnowParam

Pull Request - State: closed - Opened by Jiefei-Wang over 3 years ago - 4 comments

#179 - Disable the time limit in the worker by default

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