Posted in Research

BiocManager::install(“DNAcopy”) failed to install in r

 October 15, 2021

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: 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’

trying URL ‘bioconductor.org/packages/3.13/bioc/src/contrib/DNAcopy_1.66.0.tar.gz‘

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 bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL ‘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 bioconductor.org/packages/3.13/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL ‘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 bioconductor.org/packages/3.13/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL ‘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 bioconductor.org/packages/3.13/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL ‘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 bioconductor.org/packages/3.13/books/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL ‘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.

sessionInfo( )

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:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] stringr_1.4.0 tidyr_1.1.4 ggplot2_3.3.5 dplyr_1.0.7

loaded via a namespace (and not attached):
[1] knitr_1.36 magrittr_2.0.1 munsell_0.5.0 tidyselect_1.1.1 colorspace_2.0-2 R6_2.5.1
[7] rlang_0.4.11 fastmap_1.1.0 fansi_0.5.0 tools_4.1.1 grid_4.1.1 gtable_0.3.0
[13] xfun_0.26 utf8_1.2.2 withr_2.4.2 htmltools_0.5.2 ellipsis_0.3.2 yaml_2.2.1
[19] digest_0.6.28 tibble_3.1.5 lifecycle_1.0.1 crayon_1.4.1 purrr_0.3.4 vctrs_0.3.8
[25] glue_1.4.2 evaluate_0.14 rmarkdown_2.11 stringi_1.7.5 compiler_4.1.1 pillar_1.6.3
[31] scales_1.1.1 generics_0.1.0 pkgconfig_2.0.3

<h6>#</h6>

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.

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