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installation of package has non-zero exit status #13

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JG1ANDONLY opened this issue Feb 6, 2022 · 0 comments
Open

installation of package has non-zero exit status #13

JG1ANDONLY opened this issue Feb 6, 2022 · 0 comments

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@JG1ANDONLY
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I followed your instructions for downloading. But I get this error. Do you know how to resolve that?

BiocManager::install("vitkl/ParetoTI", dependencies = c("Depends", "Imports", "LinkingTo"))
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing github package(s) 'vitkl/ParetoTI'
Downloading GitHub repo vitkl/ParetoTI@HEAD
Installing 2 packages: edgeR, BioQC
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘edgeR’ ‘BioQC’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source packages ‘edgeR’, ‘BioQC’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/edgeR_3.36.0.tar.gz'
Content type 'application/x-gzip' length 1738194 bytes (1.7 MB)

downloaded 1.7 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/BioQC_1.22.0.tar.gz'
Content type 'application/x-gzip' length 4505195 bytes (4.3 MB)

downloaded 4.3 MB

  • installing source package ‘edgeR’ ...
    ** using staged installation
    ** libs
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_add_prior_count.cpp -o R_add_prior_count.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_calculate_cpm.cpp -o R_calculate_cpm.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_compute_apl.cpp -o R_compute_apl.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_fit_levenberg.cpp -o R_fit_levenberg.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_fit_one_group.cpp -o R_fit_one_group.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_loess_by_col.cpp -o R_loess_by_col.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
    clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c add_prior.cpp -o add_prior.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c adj_coxreid.cpp -o adj_coxreid.o
    clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fmm_spline.c -o fmm_spline.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glm_levenberg.cpp -o glm_levenberg.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glm_one_group.cpp -o glm_one_group.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.cpp -o init.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interpolator.cpp -o interpolator.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nbdev.cpp -o nbdev.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objects.cpp -o objects.o
    clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
    ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
    ld: library not found for -lgfortran
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    make: *** [edgeR.so] Error 1
    ERROR: compilation failed for package ‘edgeR’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/edgeR’
    ERROR: dependency ‘edgeR’ is not available for package ‘BioQC’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/BioQC’

The downloaded source packages are in
‘/private/var/folders/m3/_dck4dnd2rq0nggxjmg7glb80000gn/T/Rtmp6y3o3Y/downloaded_packages’
Running R CMD build...

  • checking for file ‘/private/var/folders/m3/_dck4dnd2rq0nggxjmg7glb80000gn/T/Rtmp6y3o3Y/remotes10b529932339/vitkl-ParetoTI-5109906/DESCRIPTION’ ... OK
  • preparing ‘ParetoTI’:
  • checking DESCRIPTION meta-information ... OK
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
    Omitted ‘LazyData’ from DESCRIPTION
  • building ‘ParetoTI_0.1.13.tar.gz’
    ERROR: dependency ‘BioQC’ is not available for package ‘ParetoTI’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/ParetoTI’
    Warning messages:
    1: In i.p(...) : installation of package ‘edgeR’ had non-zero exit status
    2: In i.p(...) : installation of package ‘BioQC’ had non-zero exit status
    3: In i.p(...) :
    installation of package ‘/var/folders/m3/_dck4dnd2rq0nggxjmg7glb80000gn/T//Rtmp6y3o3Y/file10b539c109e3/ParetoTI_0.1.13.tar.gz’ had non-zero exit status

library(ParetoTI)
Error in library(ParetoTI) : there is no package called ‘ParetoTI’
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@JG1ANDONLY