list installed packages
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dmahoney • 0
@2c114b29
Last seen 2.1 years ago
United States

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I am migrating an R installation on Centos to a new Ubuntu server, and I am trying to compile a list on the packages that were installed using BiocManager that will need to be installed on the new server. Using "BiocManager::install()" on the original server gives me a list of packages that need to be updated, but not a list of all of the packages already installed. Any hints?

Thanks.
# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
Installation • 825 views
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@james-w-macdonald-5106
Last seen 43 minutes ago
United States

Use dput and installed.packages.

> dput(row.names(installed.packages()))
c("abind", "acepack", "affxparser", "affy", "AffyCompatible", 
"affycoretools", "affydata", "affyio", "airway", "ALL", "amap", 
"annotate", "AnnotationDbi", "AnnotationFilter", "AnnotationForge", 
"AnnotationHub", "annotatr", "ape", "apeglm", "aplot", "aroma.light", 
"ash", "ashr", "askpass", "assertthat", "aws.s3", "aws.signature", 
"backports", "base64", "base64enc", "base64url", "batchelor", 
"BatchQC", "batchtools", "baySeq", "bbmle", "bdsmatrix", "beachmat", 
"beanplot", "beeswarm", "betareg", "BH", "BiasedUrn", "bibtex", 
"Biobase", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", 
"BiocNeighbors", "BiocParallel", "BiocSingular", "BiocStyle", 
"BiocVersion", "bioDist", "biomaRt", "biomartr", "Biostrings", 
"biovizBase", "BiSeq", "bit", "bit64", "bitops", "blob", "bookdown", 
"brew", "brio", "broom", "BSDA", "BSgenome", "bslib", "bsseq", 
"bumphunter", "cachem", "Cairo", "callr", "car", "carData", "caret",
<snip>

Then you can copy'n'paste from one server to the other. An obvious alternative is to capture that output in a variable, save as an Rdata object, and load on your new server.

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