How to install Tidyverse on Ubuntu 18.04.3 LTS (Bionic Beaver)? - r

I'm trying to install Tidyverse on a Ubuntu 18.04.3 LTS (Bionic Beaver) system, preferably in a maintainable way, such that I can execute the code examples in a related book.
I've explored posted questions related to this one, and have found the top or accepted answers did not allow me to install Tidyverse.
Install system packages
Use already compiled binaries
Install cran packages
Install readr without lock
Install system packages (in comments)
Using devtools
So now I am trying to build up an installation procedure from a state where previously-mentioned packages begin uninstalled, which currently does not work but gives a template from which answers to this question can be modifications from.
$ sudo apt-get install libssl-dev libxml2-dev libcurl4-openssl-dev
$ sudo apt-get install r-base-core r-base-dev
$ sudo apt-get install r-cran-curl r-cran-openssl r-cran-xml2
$ R
> install.packages("tidyverse")
Following the above procedure ends with the following as output in the R interactive terminal:
Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.0.tar.gz'
Content type 'application/x-gzip' length 712837 bytes (696 KB)
==================================================
downloaded 696 KB
* installing *source* package ‘tidyverse’ ...
** package ‘tidyverse’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘$.rlang_ctxt_pronoun’, ‘$.rlang_data_pronoun’, ‘$.rlang_fake_data_pronoun’, ‘$<-.quosures’, ‘$<-.rlang_ctxt_pronoun’, ‘$<-.rlang_data_pronoun’, ‘[.quosure’, ‘[.quosures’, ‘[.rlang_data_pronoun’, ‘[.rlang_envs’, ‘[.stack’, ‘[<-.quosures’, ‘[[.quosure’, ‘[[.rlang_ctxt_pronoun’, ‘[[.rlang_data_pronoun’, ‘[[.rlang_fake_data_pronoun’, ‘[[<-.quosures’, ‘[[<-.rlang_ctxt_pronoun’, ‘[[<-.rlang_data_pronoun’, ‘Math.quosure’, ‘Ops.quosure’, ‘Summary.quosure’, ‘as.character.quosure’, ‘as.list.quosures’, ‘c.quosures’, ‘c.rlang_envs’, ‘cnd_footer.default’, ‘cnd_header.default’, ‘conditionMessage.rlang_error’, ‘format.rlang_error’, ‘format.rlang_trace’, ‘length.rlang_ctxt_pronoun’, ‘length.rlang_data_pronoun’, ‘length.rlang_fake_data_pronoun’, ‘mean.quosure’, ‘median.quosure’, ‘names.rlang_ctxt_pronoun’, ‘names.rlang_data_pronoun’, ‘name [... truncated]
Error in namespaceExport(ns, exports) :
undefined exports: !!!, !!, %#%, %#%<-, %|%, %||%, :=, f_env<-, f_lhs<-, f_rhs<-, fn_body<-, fn_env<-, fn_fmls<-, fn_fmls_names<-, .data, UQ, UQS, abort, are_na, arg_match, as_box, as_box_if, as_bytes, as_character, as_closure, as_complex, as_data_mask, as_data_pronoun, as_double, as_env, as_environment, as_function, as_integer, as_label, as_list, as_logical, as_name, as_overscope, as_pairlist, as_quosure, as_quosures, as_string, as_utf8_character, base_env, bytes, bytes_along, bytes_len, call2, call_args, call_args_names, call_depth, call_fn, call_frame, call_inspect, call_modify, call_name, call_ns, call_stack, call_standardise, caller_env, caller_fn, caller_frame, calling, catch_cnd, child_env, chr, chr_along, chr_len, chr_unserialise_unicode, cnd, cnd_body, cnd_entrace, cnd_footer, cnd_header, cnd_message, cnd_muffle, cnd_signal, cnd_type, coerce_class, coerce_type, cpl, cpl_along, cpl_len, ctxt_depth, ctxt_frame, ctxt_stack, current_env, current_fn, current_frame, dbl, dbl_along, dbl_len, done, dots_definitions, dots_list, dots_n, dots_splice, dots_values, duplicate, empty_env, enexpr, enexprs, enquo, enquos, ensym, ensyms, entrace, env, env_bind, env_bind_active, env_bind_exprs, env_bind_fns, env_bind_lazy, env_binding_are_active, env_binding_are_lazy, env_binding_are_locked, env_binding_lock, env_binding_unlock, env_bury, env_clone, env_depth, env_get, env_get_list, env_has, env_inherits, env_is_locked, env_label, env_length, env_lock, env_name, env_names, env_parent, env_parents, env_poke, env_poke_parent, env_print, env_tail, env_unbind, env_unlock, error_cnd, eval_bare, eval_tidy, exec, exiting, expr, expr_deparse, expr_interp, expr_label, expr_name, expr_print, expr_text, exprs, exprs_auto_name, f_env, f_label, f_lhs, f_name, f_rhs, f_text, flatten, flatten_chr, flatten_cpl, flatten_dbl, flatten_if, flatten_int, flatten_lgl, flatten_raw, fn_body, fn_env, fn_fmls, fn_fmls_names, fn_fmls_syms, format_error_bullets, frame_position, friendly_type, get_env, get_expr, global_env, global_frame, has_length, has_name, have_name, inform, inherits_all, inherits_any, inherits_only, int, int_along, int_len, interrupt, invoke, is_atomic, is_attached, is_bare_atomic, is_bare_bytes, is_bare_character, is_bare_double, is_bare_env, is_bare_environment, is_bare_formula, is_bare_integer, is_bare_integerish, is_bare_list, is_bare_logical, is_bare_numeric, is_bare_raw, is_bare_string, is_bare_vector, is_binary_lang, is_bool, is_box, is_bytes, is_call, is_call_stack, is_callable, is_character, is_chr_na, is_closure, is_condition, is_copyable, is_cpl_na, is_dbl_na, is_definition, is_dictionaryish, is_done_box, is_double, is_empty, is_env, is_environment, is_eval_stack, is_expr, is_expression, is_false, is_formula, is_formulaish, is_frame, is_function, is_installed, is_int_na, is_integer, is_integerish, is_interactive, is_lambda, is_lang, is_lgl_na, is_list, is_logical, is_missing, is_na, is_named, is_namespace, is_node, is_node_list, is_null, is_pairlist, is_primitive, is_primitive_eager, is_primitive_lazy, is_quosure, is_quosures, is_raw, is_reference, is_scalar_atomic, is_scalar_bytes, is_scalar_character, is_scalar_double, is_scalar_integer, is_scalar_integerish, is_scalar_list, is_scalar_logical, is_scalar_raw, is_scalar_vector, is_scoped, is_spliced, is_spliced_bare, is_stack, is_string, is_symbol, is_symbolic, is_syntactic_literal, is_true, is_unary_lang, is_vector, is_weakref, is_zap, lang, lang_args, lang_args_names, lang_fn, lang_head, lang_modify, lang_name, lang_standardise, lang_tail, last_error, last_trace, lgl, lgl_along, lgl_len, list2, list_along, list_len, ll, local_bindings, local_interactive, local_options, locally, maybe_missing, message_cnd, missing_arg, modify, mut_attrs, mut_node_caar, mut_node_cadr, mut_node_car, mut_node_cdar, mut_node_cddr, mut_node_cdr, mut_node_tag, na_chr, na_cpl, na_dbl, na_int, na_lgl, names2, new_box, new_call, new_character, new_character_along, new_complex, new_complex_along, new_data_mask, new_definition, new_double, new_double_along, new_environment, new_formula, new_function, new_integer, new_integer_along, new_language, new_list, new_list_along, new_logical, new_logical_along, new_node, new_overscope, new_quosure, new_quosures, new_raw, new_raw_along, new_weakref, node, node_caar, node_cadr, node_car, node_cdar, node_cddr, node_cdr, node_poke_caar, node_poke_cadr, node_poke_car, node_poke_cdar, node_poke_cddr, node_poke_cdr, node_poke_tag, node_tag, ns_env, ns_env_name, ns_imports_env, overscope_clean, overscope_eval_next, pairlist2, parse_expr, parse_exprs, parse_quo, parse_quos, parse_quosure, parse_quosures, peek_option, peek_options, pkg_env, pkg_env_name, prepend, prim_name, push_options, qq_show, quo, quo_expr, quo_get_env, quo_get_expr, quo_is_call, quo_is_lang, quo_is_missing, quo_is_null, quo_is_symbol, quo_is_symbolic, quo_label, quo_name, quo_set_env, quo_set_expr, quo_squash, quo_text, quos, quos_auto_name, raw_along, raw_len, rep_along, rep_named, restarting, return_from, return_to, rst_abort, rst_exists, rst_jump, rst_list, rst_maybe_jump, scoped_bindings, scoped_env, scoped_envs, scoped_interactive, scoped_names, scoped_options, search_env, search_envs, seq2, seq2_along, set_attrs, set_env, set_expr, set_names, signal, splice, squash, squash_chr, squash_cpl, squash_dbl, squash_if, squash_int, squash_lgl, squash_raw, stack_trim, string, switch_class, switch_type, sym, syms, trace_back, trace_length, type_of, unbox, vec_poke_n, vec_poke_range, warn, warning_cnd, with_abort, with_bindings, with_env, with_handlers, with_interactive, with_options, with_restarts, wref_key, wref_value, zap
ERROR: lazy loading failed for package ‘tidyverse’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/tidyverse’
The downloaded source packages are in
‘/tmp/RtmpXT3xFS/downloaded_packages’
Warning message:
In install.packages("tidyverse") :
installation of package ‘tidyverse’ had non-zero exit status
It is clear from the output that the binary matches the checksum, and that the issue is related to exporting what appear to be method names from a namespace. While I am familiar with the general problem of namespace conflicts, I am unsure what is exactly happening here.
I've also tried changing step 5 to install.packages("tidyverse", dependencies = TRUE), which instead gives the following output:
Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rex’, ‘covr’, ‘feather’
trying URL 'https://cloud.r-project.org/src/contrib/rex_1.1.2.tar.gz'
Content type 'application/x-gzip' length 89430 bytes (87 KB)
==================================================
downloaded 87 KB
trying URL 'https://cloud.r-project.org/src/contrib/covr_3.4.0.tar.gz'
Content type 'application/x-gzip' length 144119 bytes (140 KB)
==================================================
downloaded 140 KB
trying URL 'https://cloud.r-project.org/src/contrib/feather_0.3.5.tar.gz'
Content type 'application/x-gzip' length 73812 bytes (72 KB)
==================================================
downloaded 72 KB
trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.0.tar.gz'
Content type 'application/x-gzip' length 712837 bytes (696 KB)
==================================================
downloaded 696 KB
* installing *source* package ‘rex’ ...
** package ‘rex’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘[.fseq’, ‘[[.fseq’, ‘print.fseq’ were declared in NAMESPACE but not found
Error in namespaceExport(ns, exports) :
undefined exports: %$%, %<>%, %>%, %T>%, n'est pas, add, and, debug_fseq, debug_pipe, divide_by, divide_by_int, equals, extract, extract2, freduce, functions, inset, inset2, is_greater_than, is_in, is_less_than, is_weakly_greater_than, is_weakly_less_than, mod, multiply_by, multiply_by_matrix, not, or, raise_to_power, set_colnames, set_names, set_rownames, subtract, undebug_fseq, use_series
ERROR: lazy loading failed for package ‘rex’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/rex’
* installing *source* package ‘feather’ ...
** package ‘feather’ successfully unpacked and MD5 sums checked
Platform is little endian. Good.
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-read.cpp -o feather-read.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-types.cpp -o feather-types.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-write.cpp -o feather-write.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/buffer.cc -o feather/buffer.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/feather-c.cc -o feather/feather-c.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/io.cc -o feather/io.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/metadata.cc -o feather/metadata.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/reader.cc -o feather/reader.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/status.cc -o feather/status.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/types.cc -o feather/types.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/writer.cc -o feather/writer.o
ar rcs libfeather.a feather/buffer.o feather/feather-c.o feather/io.o feather/metadata.o feather/reader.o feather/status.o feather/types.o feather/writer.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o feather.so RcppExports.o feather-read.o feather-types.o feather-write.o -L. -lfeather -L/usr/lib/R/lib -lR
installing to /home/galen/R/x86_64-pc-linux-gnu-library/3.4/feather/libs
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘.DollarNames.C++Object’, ‘.DollarNames.Module’, ‘print.bytes’, ‘format.Rcpp_stack_trace’, ‘str.Rcpp_stack_trace’, ‘print.Rcpp_stack_trace’ were declared in NAMESPACE but not found
Error in namespaceExport(ns, exports) :
undefined exports: Module, Rcpp.package.skeleton, populate, loadRcppModules, setRcppClass, loadRcppClass, loadModule, cppFunction, exposeClass, evalCpp, sourceCpp, compileAttributes, registerPlugin, RcppLdFlags, LdFlags, demangle, sizeof, cpp_object_initializer, cpp_object_dummy, Rcpp.plugin.maker, getRcppVersion
ERROR: lazy loading failed for package ‘feather’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/feather’
* installing *source* package ‘tidyverse’ ...
** package ‘tidyverse’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘$.rlang_ctxt_pronoun’, ‘$.rlang_data_pronoun’, ‘$.rlang_fake_data_pronoun’, ‘$<-.quosures’, ‘$<-.rlang_ctxt_pronoun’, ‘$<-.rlang_data_pronoun’, ‘[.quosure’, ‘[.quosures’, ‘[.rlang_data_pronoun’, ‘[.rlang_envs’, ‘[.stack’, ‘[<-.quosures’, ‘[[.quosure’, ‘[[.rlang_ctxt_pronoun’, ‘[[.rlang_data_pronoun’, ‘[[.rlang_fake_data_pronoun’, ‘[[<-.quosures’, ‘[[<-.rlang_ctxt_pronoun’, ‘[[<-.rlang_data_pronoun’, ‘Math.quosure’, ‘Ops.quosure’, ‘Summary.quosure’, ‘as.character.quosure’, ‘as.list.quosures’, ‘c.quosures’, ‘c.rlang_envs’, ‘cnd_footer.default’, ‘cnd_header.default’, ‘conditionMessage.rlang_error’, ‘format.rlang_error’, ‘format.rlang_trace’, ‘length.rlang_ctxt_pronoun’, ‘length.rlang_data_pronoun’, ‘length.rlang_fake_data_pronoun’, ‘mean.quosure’, ‘median.quosure’, ‘names.rlang_ctxt_pronoun’, ‘names.rlang_data_pronoun’, ‘name [... truncated]
Error in namespaceExport(ns, exports) :
undefined exports: !!!, !!, %#%, %#%<-, %|%, %||%, :=, f_env<-, f_lhs<-, f_rhs<-, fn_body<-, fn_env<-, fn_fmls<-, fn_fmls_names<-, .data, UQ, UQS, abort, are_na, arg_match, as_box, as_box_if, as_bytes, as_character, as_closure, as_complex, as_data_mask, as_data_pronoun, as_double, as_env, as_environment, as_function, as_integer, as_label, as_list, as_logical, as_name, as_overscope, as_pairlist, as_quosure, as_quosures, as_string, as_utf8_character, base_env, bytes, bytes_along, bytes_len, call2, call_args, call_args_names, call_depth, call_fn, call_frame, call_inspect, call_modify, call_name, call_ns, call_stack, call_standardise, caller_env, caller_fn, caller_frame, calling, catch_cnd, child_env, chr, chr_along, chr_len, chr_unserialise_unicode, cnd, cnd_body, cnd_entrace, cnd_footer, cnd_header, cnd_message, cnd_muffle, cnd_signal, cnd_type, coerce_class, coerce_type, cpl, cpl_along, cpl_len, ctxt_depth, ctxt_frame, ctxt_stack, current_env, current_fn, current_frame, dbl, dbl_along, dbl_len, done, dots_definitions, dots_list, dots_n, dots_splice, dots_values, duplicate, empty_env, enexpr, enexprs, enquo, enquos, ensym, ensyms, entrace, env, env_bind, env_bind_active, env_bind_exprs, env_bind_fns, env_bind_lazy, env_binding_are_active, env_binding_are_lazy, env_binding_are_locked, env_binding_lock, env_binding_unlock, env_bury, env_clone, env_depth, env_get, env_get_list, env_has, env_inherits, env_is_locked, env_label, env_length, env_lock, env_name, env_names, env_parent, env_parents, env_poke, env_poke_parent, env_print, env_tail, env_unbind, env_unlock, error_cnd, eval_bare, eval_tidy, exec, exiting, expr, expr_deparse, expr_interp, expr_label, expr_name, expr_print, expr_text, exprs, exprs_auto_name, f_env, f_label, f_lhs, f_name, f_rhs, f_text, flatten, flatten_chr, flatten_cpl, flatten_dbl, flatten_if, flatten_int, flatten_lgl, flatten_raw, fn_body, fn_env, fn_fmls, fn_fmls_names, fn_fmls_syms, format_error_bullets, frame_position, friendly_type, get_env, get_expr, global_env, global_frame, has_length, has_name, have_name, inform, inherits_all, inherits_any, inherits_only, int, int_along, int_len, interrupt, invoke, is_atomic, is_attached, is_bare_atomic, is_bare_bytes, is_bare_character, is_bare_double, is_bare_env, is_bare_environment, is_bare_formula, is_bare_integer, is_bare_integerish, is_bare_list, is_bare_logical, is_bare_numeric, is_bare_raw, is_bare_string, is_bare_vector, is_binary_lang, is_bool, is_box, is_bytes, is_call, is_call_stack, is_callable, is_character, is_chr_na, is_closure, is_condition, is_copyable, is_cpl_na, is_dbl_na, is_definition, is_dictionaryish, is_done_box, is_double, is_empty, is_env, is_environment, is_eval_stack, is_expr, is_expression, is_false, is_formula, is_formulaish, is_frame, is_function, is_installed, is_int_na, is_integer, is_integerish, is_interactive, is_lambda, is_lang, is_lgl_na, is_list, is_logical, is_missing, is_na, is_named, is_namespace, is_node, is_node_list, is_null, is_pairlist, is_primitive, is_primitive_eager, is_primitive_lazy, is_quosure, is_quosures, is_raw, is_reference, is_scalar_atomic, is_scalar_bytes, is_scalar_character, is_scalar_double, is_scalar_integer, is_scalar_integerish, is_scalar_list, is_scalar_logical, is_scalar_raw, is_scalar_vector, is_scoped, is_spliced, is_spliced_bare, is_stack, is_string, is_symbol, is_symbolic, is_syntactic_literal, is_true, is_unary_lang, is_vector, is_weakref, is_zap, lang, lang_args, lang_args_names, lang_fn, lang_head, lang_modify, lang_name, lang_standardise, lang_tail, last_error, last_trace, lgl, lgl_along, lgl_len, list2, list_along, list_len, ll, local_bindings, local_interactive, local_options, locally, maybe_missing, message_cnd, missing_arg, modify, mut_attrs, mut_node_caar, mut_node_cadr, mut_node_car, mut_node_cdar, mut_node_cddr, mut_node_cdr, mut_node_tag, na_chr, na_cpl, na_dbl, na_int, na_lgl, names2, new_box, new_call, new_character, new_character_along, new_complex, new_complex_along, new_data_mask, new_definition, new_double, new_double_along, new_environment, new_formula, new_function, new_integer, new_integer_along, new_language, new_list, new_list_along, new_logical, new_logical_along, new_node, new_overscope, new_quosure, new_quosures, new_raw, new_raw_along, new_weakref, node, node_caar, node_cadr, node_car, node_cdar, node_cddr, node_cdr, node_poke_caar, node_poke_cadr, node_poke_car, node_poke_cdar, node_poke_cddr, node_poke_cdr, node_poke_tag, node_tag, ns_env, ns_env_name, ns_imports_env, overscope_clean, overscope_eval_next, pairlist2, parse_expr, parse_exprs, parse_quo, parse_quos, parse_quosure, parse_quosures, peek_option, peek_options, pkg_env, pkg_env_name, prepend, prim_name, push_options, qq_show, quo, quo_expr, quo_get_env, quo_get_expr, quo_is_call, quo_is_lang, quo_is_missing, quo_is_null, quo_is_symbol, quo_is_symbolic, quo_label, quo_name, quo_set_env, quo_set_expr, quo_squash, quo_text, quos, quos_auto_name, raw_along, raw_len, rep_along, rep_named, restarting, return_from, return_to, rst_abort, rst_exists, rst_jump, rst_list, rst_maybe_jump, scoped_bindings, scoped_env, scoped_envs, scoped_interactive, scoped_names, scoped_options, search_env, search_envs, seq2, seq2_along, set_attrs, set_env, set_expr, set_names, signal, splice, squash, squash_chr, squash_cpl, squash_dbl, squash_if, squash_int, squash_lgl, squash_raw, stack_trim, string, switch_class, switch_type, sym, syms, trace_back, trace_length, type_of, unbox, vec_poke_n, vec_poke_range, warn, warning_cnd, with_abort, with_bindings, with_env, with_handlers, with_interactive, with_options, with_restarts, wref_key, wref_value, zap
ERROR: lazy loading failed for package ‘tidyverse’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/tidyverse’
ERROR: dependency ‘rex’ is not available for package ‘covr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/covr’
The downloaded source packages are in
‘/tmp/RtmpGxNQPL/downloaded_packages’
Warning messages:
1: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘rex’ had non-zero exit status
2: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘feather’ had non-zero exit status
3: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘tidyverse’ had non-zero exit status
4: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘covr’ had non-zero exit status
Given the above context, how can I change the above installation procedure such that it is easily maintained with package managers?
Additional Notes:
RStudio is not installed on my system.
R version information after installation with apt-get:
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

You should probably first update R (currently it is version 3.6.1-2). The documentation on how to set new repositories for R in Ubuntu is here: https://cran.r-project.org/bin/linux/ubuntu/

Related

Error using rcpp armadillo when making R package

I am trying to get into using C++ code in my R packages. I created a test package using
usethis::create_package("~/Documents/ptest")
and I then set up the C++ necessaries using
usethis::use_rcpp_armadillo("sum_func")
I then created R/test-package.R and pasted in
## usethis namespace: start
#' #useDynLib ptest, .registration = TRUE
## usethis namespace: end
NULL
## usethis namespace: start
#' #importFrom Rcpp sourceCpp
## usethis namespace: end
NULL
In sum_func.cpp I then put
//sum.cpp
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
double rcpp_sum(NumericVector v){
double sum = 0;
for(int i=0; i<v.length(); ++i){
sum += v[i];
}
return(sum);
}
I then created R/sum__func.R and put in
#' My Sum Function
#'
#' #param vec A vector of values
#'
#' #return The sum
#' #export
#'
#' #examples
#' my_sum(1:10)
my_sum <- function(vec) {
rcpp_sum(vec)
}
But then when I run devtools::load_all(".") I get
> ℹ Loading ptest Exports from
> /Users/hwarden/Documents/ptest/src/sum_func.cpp: double
> rcpp_sum(NumericVector v)
>
> /Users/hwarden/Documents/ptest/src/RcppExports.cpp updated.
> /Users/hwarden/Documents/ptest/R/RcppExports.R updated. Re-compiling
> ptest ─ installing *source* package ‘ptest’ ... ** using staged
> installation ** libs clang++ -mmacosx-version-min=10.13
> -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include'
> -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include'
> -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include'
> -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include'
> -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c sum_func.cpp -o sum_func.o clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o ptest.so RcppExports.o sum_func.o
> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0' ld:
> warning: directory not found for option '-L/usr/local/gfortran/lib'
> ld: library not found for -lgfortran clang: error: linker command
> failed with exit code 1 (use -v to see invocation) make: ***
> [ptest.so] Error 1 ERROR: compilation failed for package ‘ptest’ ─
> removing
> ‘/private/var/folders/n4/lwxlchrn2s7gvc878rw7ln1m0000gn/T/RtmpjJw195/devtools_install_c9e2c847f68/ptest’
> Error in `(function (command = NULL, args = character(),
> error_on_status = TRUE, …`: ! System command 'R' failed
> --- Exit status: 1 stdout & stderr: <printed>
> ---
I get an error but after googling I can't figure out how to solve it.
Thank you #dirk-eddelbuettel,
This article was the most useful.
I'm not an expert, but for me this worked (or at least got me to my next error).
I ran
brew reinstall gcc
to make sure I had the most up to date gfortran. Then I made a ~/.R/Makevars (as I did not have one already). I then wrote this in there
FC = usr/local/opt/gcc/bin/gfortran
F77 = /usr/local/opt/gcc/bin/gfortran
FLIBS = -L/usr/local/opt/gcc/lib
I restarted R and the package then loaded successfully! Many thanks!

Having trouble installing R package httpuv

I am using R 3.3.3 on Debian/Linux 8 and I am having trouble installing the package httpuv, which is a dependency for another package I want to use. The installing error message is shown below. It seems like there are problems with libuv, but I am not sure about this.
How can I figure out where the problem is and how to fix it?
> install.packages("httpuv")
Installing package into ‘/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/httpuv_1.5.1.tar.gz'
Content type 'unknown' length 1758514 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** libs
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports-legacy.cpp -o RcppExports-legacy.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c callback.cpp -o callback.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c callbackqueue.cpp -o callbackqueue.o
In file included from libuv/include/uv.h:62:0,
from thread.h:4,
from tqueue.h:7,
from callbackqueue.h:4,
from callbackqueue.cpp:1:
libuv/include/uv/unix.h:103:28: error: ‘sem_t’ does not name a type
# define UV_PLATFORM_SEM_T sem_t
^
libuv/include/uv/unix.h:135:9: note: in expansion of macro ‘UV_PLATFORM_SEM_T’
typedef UV_PLATFORM_SEM_T uv_sem_t;
^
In file included from thread.h:4:0,
from tqueue.h:7,
from callbackqueue.h:4,
from callbackqueue.cpp:1:
libuv/include/uv.h:1562:27: error: ‘uv_sem_t’ was not declared in this scope
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1562:37: error: ‘sem’ was not declared in this scope
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1562:42: error: expected primary-expression before ‘unsigned’
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1562:60: error: expression list treated as compound expression in initializer [-fpermissive]
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1563:31: error: variable or field ‘uv_sem_destroy’ declared void
UV_EXTERN void uv_sem_destroy(uv_sem_t* sem);
^
libuv/include/uv.h:1563:31: error: ‘uv_sem_t’ was not declared in this scope
libuv/include/uv.h:1563:41: error: ‘sem’ was not declared in this scope
UV_EXTERN void uv_sem_destroy(uv_sem_t* sem);
^
libuv/include/uv.h:1564:28: error: variable or field ‘uv_sem_post’ declared void
UV_EXTERN void uv_sem_post(uv_sem_t* sem);
^
libuv/include/uv.h:1564:28: error: ‘uv_sem_t’ was not declared in this scope
libuv/include/uv.h:1564:38: error: ‘sem’ was not declared in this scope
UV_EXTERN void uv_sem_post(uv_sem_t* sem);
^
libuv/include/uv.h:1565:28: error: variable or field ‘uv_sem_wait’ declared void
UV_EXTERN void uv_sem_wait(uv_sem_t* sem);
^
libuv/include/uv.h:1565:28: error: ‘uv_sem_t’ was not declared in this scope
libuv/include/uv.h:1565:38: error: ‘sem’ was not declared in this scope
UV_EXTERN void uv_sem_wait(uv_sem_t* sem);
^
libuv/include/uv.h:1566:30: error: ‘uv_sem_t’ was not declared in this scope
UV_EXTERN int uv_sem_trywait(uv_sem_t* sem);
^
libuv/include/uv.h:1566:40: error: ‘sem’ was not declared in this scope
UV_EXTERN int uv_sem_trywait(uv_sem_t* sem);
^
/usr/lib/R/etc/Makeconf:141: recipe for target 'callbackqueue.o' failed
make: *** [callbackqueue.o] Error 1
ERROR: compilation failed for package ‘httpuv’
* removing ‘/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/httpuv’
The downloaded source packages are in
‘/tmp/Rtmpqg62zZ/downloaded_packages’
Warning message:
In install.packages("httpuv") :
installation of package ‘httpuv’ had non-zero exit status
I had the same error and tried several installations to make it work:
Install Java jre and jdk
Install devtools install.packages("devtools")
In the console, run .libPaths() to see where packages are installed.
Make sure to get full permission from your library directory
Run devtools::install_github("rstudio/httpuv", lib = "directory from 3.") in the console.

R Rstudio problems installing packages mapdeck and googlePolylines

When I try to install the package mapdeck in Rstudio, it appears a message in the console saying that I need to install the package googlePolylines, but I can't install this one. The error that appears in the console is the following:
package ‘googlePolylines’ successfully unpacked and MD5 sums checked
libs
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I../inst/include -I"/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I../inst/include -I"/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c encode.cpp -o encode.o
encode.cpp: In function ‘void encode_vector(std::ostringstream&, std::ostringstream&, Rcpp::List, Rcpp::CharacterVector&, int)’:
encode.cpp:175: error: conversion from ‘Rcpp::internal::generic_proxy<19, Rcpp::PreserveStorage>’ to ‘double’ is ambiguous
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:73: note: candidates are: Rcpp::internal::generic_proxy::operator int() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:72: note: Rcpp::internal::generic_proxy::operator bool() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:67: note: Rcpp::internal::generic_proxy::operator U() const [with U = double, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
encode.cpp:176: error: conversion from ‘Rcpp::internal::generic_proxy<19, Rcpp::PreserveStorage>’ to ‘double’ is ambiguous
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:73: note: candidates are: Rcpp::internal::generic_proxy::operator int() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:72: note: Rcpp::internal::generic_proxy::operator bool() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:67: note: Rcpp::internal::generic_proxy::operator U() const [with U = double, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
make: *** [encode.o] Error 1
ERROR: compilation failed for package ‘googlePolylines’
removing ‘/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/googlePolylines’
Warning in install.packages :
installation of package ‘googlePolylines’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpwwAJSv/downloaded_packages’
I haven't found almost any information about these two packages, so I would appreciate if anyone could help me, thank you.

cannot install rgdal package in local server, An irrecoverable exception occurred. R is aborting now...[ERROR: loading failed]

I'm trying to install Rgdal package, all packages and their dependancies I've installed them manuelly since my server is offline, I have struggled with those dependancies for a long time. but now I think I fix the problem, but my problem now I think has came from R, I cannot even figure out what's happen. this is the out put I gut when I run the commande install.packages("rgdal_1.2-15.tar.gz","/usr/lib64/R/library/",repos=NULL,configure.args="--with-proj-include=/usr/proj49/include/") on R:
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: CC: gcc -m64 -std=gnu99
configure: CXX: g++ -m64
configure: rgdal: 1.2-15
checking for /usr/bin/svnversion... no
configure: svn revision: 691
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.8.1
checking GDAL version >= 1.6.3... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... yes
configure: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/proj49/include/
checking proj_api.h presence and usability... yes
checking PROJ.4 version: ... > 4.8.0
/usr/bin/ld: warning: libproj.so.12, needed by /usr/lib64/libogdi.so.3, may conflict with libproj.so.0
./configure: line 2112: 27095 Segmentation fault (core dumped) ./proj_conf_test2
checking PROJ.4: epsg found and readable... yes
/usr/bin/ld: warning: libproj.so.12, needed by /usr/lib64/libogdi.so.3, may conflict with libproj.so.0
./configure: line 2187: 27107 Segmentation fault (core dumped) ./proj_conf_test3
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags: -I/usr/include/gdal -I/usr/proj49/include/
configure: Package LIBS: -lgdal -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c OGR_write.cpp -o OGR_write.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c gdal-bindings.cpp -o gdal-bindings.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c init.c -o init.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c inverser.c -o inverser.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c local_stubs.c -o local_stubs.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogr_geom.cpp -o ogr_geom.o
ogr_geom.cpp: In function ‘SEXPREC* R_OGR_CAPI_features(SEXPREC*, SEXPREC*, SEXPREC*)’:
ogr_geom.cpp:39: warning: ‘mp_count_k0’ may be used uninitialized in this function
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c ogr_polygons.c -o ogr_polygons.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogr_proj.cpp -o ogr_proj.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogrdrivers.cpp -o ogrdrivers.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogrsource.cpp -o ogrsource.o
ogrsource.cpp: In function ‘SEXPREC* ogrReadListColumn(OGRLayer*, SEXPREC*, int, int, int)’:
ogrsource.cpp:651: warning: unused variable ‘DINT_MAX’
ogrsource.cpp:652: warning: unused variable ‘DINT_MIN’
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c projectit.cpp -o projectit.o
g++ -m64 -std=c++0x -shared -L/usr/lib64/R/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -lgdal -lproj -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/rgdal/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package ‘rgdal’
finding HTML links ... done
CRS-class html
GDALDataset-class html
GDALDriver-class html
GDALMajorObject-class html
GDALRasterBand-class html
GDALReadOnlyDataset-class html
GDALReadOnlyDataset-methods html
GDALTransientDataset-class html
GridsDatums html
RGB2PCT html
SGDF2PCT html
SpatialGDAL-class html
closeDataset-methods html
displayDataset html
llgrid html
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/llgrid.Rd:11: missing file link ‘Spatial’
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/llgrid.Rd:16: missing file link ‘gridat’
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/llgrid.Rd:17: missing file link ‘gridat’
make_EPSG html
nor2k html
projInfo html
project html
readGDAL html
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/readGDAL.Rd:136: missing file link ‘flipVertical’
readOGR html
showWKT html
spTransform-methods html
wrappers html
writeOGR html
** building package indices
** installing vignettes
** testing if installed package can be loaded
sh: line 1: 28842 Segmentation fault (core dumped) '/usr/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpKNPZgP/file68d75bc50ad1'
*** caught segfault ***
address 0x20, cause 'memory not mapped'
Traceback:
1: .Call("PROJ4_proj_def_dat_Installed", PACKAGE = "rgdal")
2: assign("has_proj_def.dat", .Call("PROJ4_proj_def_dat_Installed", PACKAGE = "rgdal"), envir = .RGDAL_CACHE)
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
14: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)})
15: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
16: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
17: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
22: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
23: tools:::.test_load_package("rgdal", "/usr/lib64/R/library")
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing ‘/usr/lib64/R/library/rgdal’
Warning message:
In install.packages("rgdal_1.2-15.tar.gz", "/usr/lib64/R/library/", :
installation of package ‘rgdal_1.2-15.tar.gz’ had non-zero exit status
Update:
even with a newer version of Rgdal install.packages("rgdal_1.2-18.tar.gz","/usr/lib64/R/library/",repos=NULL,configure.args="--with-proj-include=/usr/proj49/include/"), I got the same error
Please follow the below steps to install gdal on RHEL/CentOS 7
wget http://download.osgeo.org/gdal/2.0.1/gdal-2.0.1.tar.gz
./configure
make
make install

Error when installing TDA package on R: recipe for target 'diag.o' failed

Using Ubuntu 16.04 and R 3.4.1. I get an error message when installing R package TDA. It appears to be something with making CGAL, diag.cpp, and/or diag.o (full error printout at end).
I looked closely at this:
Error when installing TDA package on R
but I have libgmp3-dev and libmpfr-dev installed (I tried removing them and then I did get that error message). I also tried removing and manually installing the Imports and LinkingTo packages for TDA (https://cran.r-project.org/web/packages/TDA/index.html), but no luck. Also tried
running R with sudo and install.packages
downloading the binaries and installing with sudo R CMD INSTALL TDA
installing CGAL
Any help appreciated.
install.packages("TDA")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.revolutionanalytics.com/src/contrib/TDA_1.5.1.tar.gz'
Content type 'application/octet-stream' length 2008762 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘TDA’ ...
** package ‘TDA’ successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I/usr/share/R/include -I. -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/BH/include" -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/usr/share/R/include -I. -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/BH/include" -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c diag.cpp -o diag.o
In file included from ./CGAL/Triangulation_ds_cell_base_3.h:27:0,
from ./CGAL/Triangulation_data_structure_3.h:47,
from ./CGAL/Triangulation_3.h:43,
from ./CGAL/Delaunay_triangulation_3.h:37,
from ./tdautils/cgalUtils.h:5,
from diag.cpp:25:
./CGAL/Triangulation_ds_cell_base_3.h: In instantiation of ‘void CGAL::Triangulation_ds_cell_base_3<TDS>::set_neighbor(int, CGAL::Triangulation_ds_cell_base_3<TDS>::Cell_handle) [with TDS = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; CGAL::Triangulation_ds_cell_base_3<TDS>::Cell_handle = CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Default, CGAL::Default, CGAL::Default>, false>]’:
./CGAL/Triangulation_data_structure_3.h:2782:7: required from ‘CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::Vertex_handle CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::insert_increase_dimension(CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::Vertex_handle) [with Vb = CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>; Cb = CGAL::Alpha_shape_cell_base_3<CGAL::Epick>; Concurrency_tag_ = CGAL::Sequential_tag; CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::Vertex_handle = CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, CGAL::Triangulation_vertex_base_3<CGAL::Epick, CGAL::Triangulation_ds_vertex_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Default, CGAL::Default, CGAL::Default>, false>]’
./CGAL/Triangulation_3.h:623:16: required from ‘void CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::init_tds() [with GT = CGAL::Epick; Tds_ = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; Lock_data_structure_ = CGAL::Default]’
./CGAL/Triangulation_3.h:655:15: required from ‘CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Triangulation_3(const GT&, CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Lock_data_structure*) [with GT = CGAL::Epick; Tds_ = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; Lock_data_structure_ = CGAL::Default; CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Lock_data_structure = void]’
./CGAL/Delaunay_triangulation_3.h:229:26: required from ‘CGAL::Delaunay_triangulation_3<Gt, Tds_, CGAL::Default, Lock_data_structure_>::Delaunay_triangulation_3(const Gt&, CGAL::Delaunay_triangulation_3<Gt, Tds_, CGAL::Default, Lock_data_structure_>::Lock_data_structure*) [with Gt = CGAL::Epick; Tds_ = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; Lock_data_structure_ = CGAL::Default; CGAL::Delaunay_triangulation_3<Gt, Tds_, CGAL::Default, Lock_data_structure_>::Lock_data_structure = void]’
./CGAL/Alpha_shape_3.h:263:51: required from ‘CGAL::Alpha_shape_3<Dt, ExactAlphaComparisonTag>::Alpha_shape_3(const InputIterator&, const InputIterator&, const NT&, CGAL::Alpha_shape_3<Dt, ExactAlphaComparisonTag>::Mode) [with InputIterator = std::_List_iterator<CGAL::Point_3<CGAL::Epick> >; Dt = CGAL::Delaunay_triangulation_3<CGAL::Epick, CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > >; ExactAlphaComparisonTag = CGAL::Boolean_tag<false>; CGAL::Alpha_shape_3<Dt, ExactAlphaComparisonTag>::NT = double]’
diag.cpp:680:65: required from here
./CGAL/Triangulation_ds_cell_base_3.h:166:39: error: ‘class CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >’ has no member named ‘operator()’
CGAL_triangulation_precondition(this != n->operator());
^
./CGAL/triangulation_assertions.h:130:20: note: in definition of macro ‘CGAL_triangulation_precondition’
(CGAL::possibly(EX)?(static_cast<void>(0)): ::CGAL::precondition_fail( # EX
^
/usr/lib/R/etc/Makeconf:168: recipe for target 'diag.o' failed
make: *** [diag.o] Error 1
ERROR: compilation failed for package ‘TDA’
* removing ‘/usr/local/lib/R/site-library/TDA’
The downloaded source packages are in
‘/tmp/RtmpFqA1Fu/downloaded_packages’
Warning message:
In install.packages("TDA") :
installation of package ‘TDA’ had non-zero exit status
>
TDA v1.5.1 has the same issue on my Linux servers. Try install a previous version:
install.packages("devtools")
require(devtools);
install_version('TDA', version='1.4.1')

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