Cannot install bioconductor packages

I need to work with some bioconductor packages, but i cannot install those required packages.

1: In install.packages(...) :
installation of package ‘fgsea’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘SummarizedExperiment’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘oligoClasses’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘beadarray’ had non-zero exit status
5: In install.packages(...) :
installation of package ‘oligo’ had non-zero exit status
6: In install.packages(...) :
installation of package ‘ArrayExpress’ had non-zero exit status
7: In install.packages(...) :
installation of package ‘pd.hugene.1.0.st.v1’ had non-zero exit status
8: In install.packages(...) :
installation of package ‘genefilter’ had non-zero exit status
9: In install.packages(...) :
installation of package ‘DOSE’ had non-zero exit status
10: In install.packages(...) :
installation of package ‘arrayQualityMetrics’ had non-zero exit status
11: In install.packages(...) :
installation of package ‘enrichplot’ had non-zero exit status
12: In install.packages(...) :
installation of package ‘ReactomePA’ had non-zero exit status
13: In install.packages(...) :
installation of package ‘clusterProfiler’ had non-zero exit status
14: In install.packages(...) :
installation of package ‘maEndToEnd’ had non-zero exit status

There is a (recommended](Bioconductor - Install) installation manager using the {bioconducter}) package.

1 Like

You can also try pak, which supports Bioconductor packages OOTB:

install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
pak::pkg_install("fgsea")
✔ Loading metadata database ... done
→ Will install 1 package.
→ Will download 1 package with unknown size.
+ fgsea   1.24.0  ⬇
ℹ Getting 1 pkg with unknown size
✔ Got fgsea 1.24.0 (aarch64-apple-darwin20) (4.34 MB)
✔ Downloaded 1 package (4.34 MB)in 1.2s
✔ Installed fgsea 1.24.0  (49ms)
✔ 1 pkg + 39 deps: kept 38, added 1, dld 1 (4.34 MB) [7.2s]
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