Question: genbankr not working because rtracklayer does not install
5 months ago by
dmontecino • 0
dmontecino • 0 wrote:
I tried to install genbankr but I had issues with the rtracklayer package:
this is what I did.
Could you please help me how to make it work.
Thanks for all the amazing resources provided
> library("genbankr") Error: package or namespace load failed for ‘genbankr’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘rtracklayer’ > if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") > > BiocManager::install("rtracklayer") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'rtracklayer' There is a binary version available but the source version is later: binary source needs_compilation rtracklayer 1.43.3 1.44.0 TRUE Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Y installing the source package ‘rtracklayer’ trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/rtracklayer_1.44.0.tar.gz' Content type 'application/x-gzip' length 1540317 bytes (1.5 MB) ================================================== downloaded 1.5 MB * installing *source* package ‘rtracklayer’ ... ** using staged installation checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2d_1/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot] In file included from S4Vectors_stubs.c:1: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include/_S4Vectors_stubs.c:1: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include/S4Vectors_interface.h:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include/S4Vectors_defines.h:18: In file included from /Library/Frameworks/R.framework/Resources/include/Rdefines.h:37: /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:34:11: fatal error: 'string.h' file not found # include <string.h> /* for memcpy, memset */ ^~~~~~~~~~ 1 error generated. make: *** [S4Vectors_stubs.o] Error 1 ERROR: compilation failed for package ‘rtracklayer’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rtracklayer’ The downloaded source packages are in ‘/private/var/folders/55/drdb0yv54yx3nljl3p44tl_c0000gn/T/Rtmp3e8E19/downloaded_packages’ Warning message: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘rtracklayer’ had non-zero exit status > library("genbankr") Error: package or namespace load failed for ‘genbankr’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘rtracklayer’
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