search for: biocmanag

Lauren, On 15 October 2024 at 13:51, Gerber, Lauren J wrote: | I just tried fixing my script and added library(BiocManager) before library | (ggbreak), then rebuilt the image, and am still getting the same error. You need _two_ distinct commands. First install.packages("BiocManager") and second once that is done use it to install 'ggbreak' from BioConductor BiocManager::install("ggr...

...lready_installed)){ packageStartupMessage("Need to install the following package(s): ", toString(toinstall[!already_installed]), "\n") } ## install if needed if(!base::all(already_installed)){ if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(toinstall[!already_installed], dependencies=TRUE) } } [[alternative HTML version deleted]]

...1/2019 6:17 p.m., Henrik Bengtsson wrote: > I believe introducing a backward compatible force=TRUE is a good > start, even if we're not ready for making force=FALSE the default at > this point. It would help simplify quite-common instructions like > > if (requireNamespace("BiocManager")) > install.packages("BiocManager") > BiocManager::install(...) > > to > > install.packages("BiocManager", force=FALSE) > BiocManager::install(...) If simplifying instructions is the goal, it would be even simpler to just install it unconditio...

Don't you have to load BiocManager before using it? -----Original Message----- From: R-SIG-Debian <r-sig-debian-bounces at r-project.org> On Behalf Of Gerber, Lauren J Sent: Tuesday, October 15, 2024 9:15 AM To: r-sig-debian at r-project.org Cc: dirk at eddelbuettel.com Subject: Re: [R-sig-Debian] R Package: 'ggbreak...

Hi James, I just tried fixing my script and added library(BiocManager) before library(ggbreak), then rebuilt the image, and am still getting the same error. Error in library(ggbreak) : there is no package called 'ggbreak' Execution halted I will say that when I ran docker exec docker_container_id R -e "installed.packages()" I get the following:...

...Bengtsson wrote: > > I believe introducing a backward compatible force=TRUE is a good > > start, even if we're not ready for making force=FALSE the default at > > this point. It would help simplify quite-common instructions like > > > > if (requireNamespace("BiocManager")) > > install.packages("BiocManager") > > BiocManager::install(...) > > > > to > > > > install.packages("BiocManager", force=FALSE) > > BiocManager::install(...) > > If simplifying instructions is the goal, it would be e...

Hi Gabe, Keeping track of where a package was installed from would be a nice feature. However it wouldn't be as reliable as comparing hashes to decide whether a package needs re-installation or not. H. On 11/8/19 12:37, Gabriel Becker wrote: > Hi Josh, > > There are a few issues I can think of with this. The primary one is that > CRAN(/Bioconductor) is not the only place one

...motes::install_github('YuLab-SMU/ggbreak')" RUN R -e "install.packages('ggrepel', repos='http://cran.us.r-project.org')" RUN R -e "install.packages('stringr', repos='http://cran.us.r-project.org')" RUN R -e "install.packages('BiocManager', repos='http://cran.us.r-project.org')" RUN R -e "BiocManager::install('ggbreak')" # Create an app directory RUN mkdir /app RUN mkdir /volume_w_htmls RUN mkdir /volume RUN mkdir /volume2 RUN mkdir /home/seluser/Downloads # Set the working directory WORKDIR /a...

I believe introducing a backward compatible force=TRUE is a good start, even if we're not ready for making force=FALSE the default at this point. It would help simplify quite-common instructions like: if (requireNamespace("BiocManager")) install.packages("BiocManager") BiocManager::install(...) to install.packages("BiocManager", force=FALSE) BiocManager::install(...) and more so when installing lots of packages conditionally, e.g. if (requireNamespace("foo")) install.packages("foo&...

...emp file. If I use ` gzfile` to read the file, it can show the first 1000 lines successfully. However, if I wrap the raw vector as a connection, and use `gzcon` to read from that connection, it shows the first 884 lines along with a warning(see the output). code: > # installed.packages("BiocManager") > # BiocManager::install("GCSConnection", version = "devel") > library(GCSConnection) > ## Download data from cloud > uri <- > "gs://gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.chr1.vcf.bgz" > con <- gcs_connection(u...

...r-base\ && apt-get clean \ && apt-get purge \ && rm -rf /var/lib/apt/lists/* /tmp/* ## Configure parallel options to use max CPUs by default and install BioC RUN /usr/bin/R -e 'options(Ncpus = parallel::detectCores())'\ -e 'install.packages("BiocManager")' \ -e 'BiocManager::install()' Marco From: Gerber, Lauren J <lauren.gerber at helsinki.fi> Date: Wednesday, July 10, 2024 at 9:43?AM To: Dirk Eddelbuettel <edd at debian.org> Cc: Dirk Eddelbuettel <edd at debian.org>, marcoblanchette at icloud.com <ma...

...r-base\ && apt-get clean \ && apt-get purge \ && rm -rf /var/lib/apt/lists/* /tmp/* ## Configure parallel options to use max CPUs by default and install BioC RUN /usr/bin/R -e 'options(Ncpus = parallel::detectCores())'\ -e 'install.packages("BiocManager")' \ -e 'BiocManager::install()' Marco From: Gerber, Lauren J <lauren.gerber at helsinki.fi> Date: Wednesday, July 10, 2024 at 9:43?AM To: Dirk Eddelbuettel <edd at debian.org> Cc: Dirk Eddelbuettel <edd at debian.org>, marcoblanchette at icloud.com <ma...

...r-base\ && apt-get clean \ && apt-get purge \ && rm -rf /var/lib/apt/lists/* /tmp/* ## Configure parallel options to use max CPUs by default and install BioC RUN /usr/bin/R -e 'options(Ncpus = parallel::detectCores())'\ -e 'install.packages("BiocManager")' \ -e 'BiocManager::install()' Marco From: Gerber, Lauren J <lauren.gerber at helsinki.fi> Date: Wednesday, July 10, 2024 at 9:43?AM To: Dirk Eddelbuettel <edd at debian.org> Cc: Dirk Eddelbuettel <edd at debian.org>, marcoblanchette at icloud.com <ma...

Hi Dirk, Thank you so much for looking into this when you got home. I greatly appreciate it. I was actually in the midst of writing to everyone the following message: ?. ?. ?. Hi All, I have some good news. ? My docker image is now up-to-date with R version 4.4.1. I first had to clear a bunch of unused data using docker system prune ?force. Apparently, it cleared over 32.53 gigs of data, and

...r-base\ && apt-get clean \ && apt-get purge \ && rm -rf /var/lib/apt/lists/* /tmp/* ## Configure parallel options to use max CPUs by default and install BioC RUN /usr/bin/R -e 'options(Ncpus = parallel::detectCores())'\ -e 'install.packages("BiocManager")' \ -e 'BiocManager::install()' From: R-SIG-Debian <r-sig-debian-bounces at r-project.org> on behalf of Gerber, Lauren J <lauren.gerber at helsinki.fi> Date: Monday, July 8, 2024 at 6:08?AM To: r-sig-debian at r-project.org <r-sig-debian at r-project.org&gt...

Hi All, I am building a Docker image that uses Ubuntu 22.04 and am having issues installing the latest version of R (R 4.4.1). The current R version is 4.1.2: :/# apt-cache policy r-base-core r-base-core: Installed: 4.1.2-1ubuntu2 Candidate: 4.1.2-1ubuntu2 Version table: *** 4.1.2-1ubuntu2 500 500 http://archive.ubuntu.com/ubuntu jammy/universe amd64 Packages 100