Enter the body of text here
Code should be placed in three backticks as shown below
BiocManager::install("DNAcopy") # include your problematic code here with any corresponding output
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: https://cran.rstudio.com/
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) Installing package(s) 'DNAcopy' Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘DNAcopy’ Do you want to attempt to install these from sources? (Yes/no/cancel) yes installing the source package ‘DNAcopy’
Content type 'application/x-gzip' length 319566 bytes (312 KB)
downloaded 312 KB
- installing source package ‘DNAcopy’ ... using staged installation libs /opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c cbsWtstats.f -o cbsWtstats.o make: /opt/R/arm64/bin/gfortran: Permission denied make: *** [cbsWtstats.o] Error 1 ERROR: compilation failed for package ‘DNAcopy’
- removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/DNAcopy’
The downloaded source packages are in ‘/private/var/folders/0r/hfzd3wtx0fn5qj94dr7_6zg00000gn/T/RtmpyUdSc7/downloaded_packages’ Warning messages: 1: In .inet_warning(msg) : unable to access index for repository https://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' 2: In .inet_warning(msg) : unable to access index for repository https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' 3: In .inet_warning(msg) : unable to access index for repository https://bioconductor.org/packages/3.13/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.13/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' 4: In .inet_warning(msg) : unable to access index for repository https://bioconductor.org/packages/3.13/workflows/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.13/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' 5: In .inet_warning(msg) : unable to access index for repository https://bioconductor.org/packages/3.13/books/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.13/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' 6: In .inet_warning(msg) : installation of package ‘DNAcopy’ had non-zero exit status
By the way, I manually downloaded gfortran and installed locally. Before I installed gfortran under /opt/R/arm64/bin/, the error message was "gfortran is not found /opt/R/arm64/bin/ "
(base) limin@DERM-6NBQ05N-LT bin % which gfortran /usr/local/bin/gfortran (base) limin@DERM-6NBQ05N-LT bin % gfortran --version GNU Fortran (GCC) 11.0.0 20201205 (experimental) Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
please also include the results of running the following in an R session
R version 4.1.1 (2021-08-10) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Big Sur 11.5.1
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:  stats graphics grDevices utils datasets methods base
other attached packages:  stringr_1.4.0 tidyr_1.1.4 ggplot2_3.3.5 dplyr_1.0.7
loaded via a namespace (and not attached):
 knitr_1.36 magrittr_2.0.1 munsell_0.5.0 tidyselect_1.1.1 colorspace_2.0-2 R6_2.5.1
 rlang_0.4.11 fastmap_1.1.0 fansi_0.5.0 tools_4.1.1 grid_4.1.1 gtable_0.3.0
 xfun_0.26 utf8_1.2.2 withr_2.4.2 htmltools_0.5.2 ellipsis_0.3.2 yaml_2.2.1
 digest_0.6.28 tibble_3.1.5 lifecycle_1.0.1 crayon_1.4.1 purrr_0.3.4 vctrs_0.3.8
 glue_1.4.2 evaluate_0.14 rmarkdown_2.11 stringi_1.7.5 compiler_4.1.1 pillar_1.6.3
 scales_1.1.1 generics_0.1.0 pkgconfig_2.0.3
Here is my mac information: macOS Big Sur, Version 11.5.1 MacBook Pro(M1, 2020) Chip Apple M1
PS: I actually want to install PSCBS which requires DNAcopy installed first. But failed to install DNAcopy.
Thanks for all the help in advance.