At wit's end after updating to latest: my Ubuntu 16.04LTS update/upgrades, my R version, my Rstudio-server version, my libicu-dev version, verified that anaconda is providing my python but not my R language. What else can help? This stringi package might also be at the root of my new problems (didn't have problems before) of not being able to create an r markdown document (looks like Knittr uses stringi), jupyter notebook with R language, not being able to install ggplot2, etc etc.
g++ is already the newest version (4:5.3.1-1ubuntu1)
libicu-dev is already the newest version (55.1-7ubuntu0.2)
Here is the rstudio console output (long):
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages("stringi")
Installing package into ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /usr/lib/R
checking for R... /usr/lib/R/bin/R
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... no
checking for cat... /bin/cat
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /usr/bin/pkg-config
checking with pkg-config for the system ICU4C... 55.1
checking for ICU4C >= 52... yes
checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done
checking whether we may build an ICU4C-based project... yes
checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes
checking for available ICU data library (ucnv, uloc, utrans)... yes
checking for available ICU data library (ucol)... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R
*** stringi configure summary:
ICU_FOUND=1
STRINGI_CXXSTD=CXX_STD=CXX11
STRINGI_CFLAGS= -fpic
STRINGI_CPPFLAGS=-I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H
STRINGI_CXXFLAGS= -fpic
STRINGI_LDFLAGS=-L/usr/lib/x86_64-linux-gnu
STRINGI_LIBS=-licui18n -licuuc -licudata
*** compiler settings used:
CC=gcc -std=gnu99
CPP=g++ -E
LD=g++
CFLAGS=-I/usr/lib/x86_64-linux-gnu -fpic
CPPFLAGS= -UDEBUG -DNDEBUG
CXX=g++ -std=gnu++11
CXXFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic
LDFLAGS=
LIBS=
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_brkiter.cpp -o stri_brkiter.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_collator.cpp -o stri_collator.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_common.cpp -o stri_common.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_compare.cpp -o stri_compare.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_base.cpp -o stri_container_base.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o
...(snip)...
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_in.cpp -o stri_search_in.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_other_replace.cpp -o stri_search_other_replace.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_other_split.cpp -o stri_search_other_split.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_count.cpp -o stri_search_regex_count.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_match.cpp -o stri_search_regex_match.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_split.cpp -o stri_search_regex_split.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_sort.cpp -o stri_sort.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stats.cpp -o stri_stats.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stringi.cpp -o stri_stringi.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_sub.cpp -o stri_sub.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_test.cpp -o stri_test.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_zone.cpp -o stri_time_zone.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_calendar.cpp -o stri_time_calendar.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_symbols.cpp -o stri_time_symbols.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_format.cpp -o stri_time_format.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_casemap.cpp -o stri_trans_casemap.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_other.cpp -o stri_trans_other.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_normalization.cpp -o stri_trans_normalization.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_ucnv.cpp -o stri_ucnv.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_uloc.cpp -o stri_uloc.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_utils.cpp -o stri_utils.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_wrap.cpp -o stri_wrap.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -L/usr/lib/x86_64-linux-gnu -lgsl -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_replace.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_stats.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib/x86_64-linux-gnu -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/ga/R/x86_64-pc-linux-gnu-library/3.4/stringi
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘stringi’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/ga/R/x86_64-pc-linux-gnu-library/3.4/stringi/libs/stringi.so':
/home/ga/R/x86_64-pc-linux-gnu-library/3.4/stringi/libs/stringi.so: undefined symbol: _ZTIN6icu_558ByteSinkE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.4/stringi’
Warning in install.packages :
installation of package ‘stringi’ had non-zero exit status
ARe there some other diagnostics to try? BTW stringi worked fine in R3.3 but now I have R3.4.