BiocManager::install("DNAcopy") failed to install in r
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Limin • 0
@07154eaf
Last seen 7 weeks ago
United States

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’

trying URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/DNAcopy_1.66.0.tar.gz'

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

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.

DNAcopy R • 129 views
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0
Entering edit mode
Mike Smith ★ 5.2k
@mike-smith
Last seen 16 hours ago
EMBL Heidelberg / de.NBI

It looks like there's some permissions problems with the gfortran you've installed.

When you've run which gfortran you get back /usr/local/bin/gfortran. However the error message shows make: /opt/R/arm64/bin/gfortran: Permission denied, so these are not necessarily the same instances of gfortan. Do you have permission to run /opt/R/arm64/bin/gfortran --version ?


Possibly an easier strategy is to install R for Intel CPUs and run it with Rosetta. Then you'll be able to use the binary versions of packages that Bioconductor builds, and you won't have to worry about compiling anything from source.

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