Question: genbankr not working because rtracklayer does not install
0
gravatar for dmontecino
6 weeks ago by
dmontecino0
dmontecino0 wrote:

Hi:

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’
genbankr rtracklayer • 82 views
ADD COMMENTlink written 6 weeks ago by dmontecino0
1

What happens if you select 'no' and let it install the binary version?

ADD REPLYlink written 6 weeks ago by Mike Smith3.8k

I had the same issue as dmontecino and entering n at the prompt "Do you want to install from sources the package which needs compilation? (Yes/no/cancel)" worked for me. Thanks, Mike!

ADD REPLYlink written 29 days ago by bmarieg0
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