Issues during installation on RHEL 6

[arnonerba]

Lubridate 1.7.0 will not install or update on Red Hat Enterprise Linux 6 (version 1.6.0 was previously installed and working):

install.packages("lubridate")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/lubridate_1.7.0.tar.gz'
Content type 'application/x-gzip' length 398375 bytes (389 KB)
==================================================
downloaded 389 KB

• installing source package ‘lubridate’ ...
  ** package ‘lubridate’ successfully unpacked and MD5 sums checked
  ** libs
  g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/usr/lib64/R/library/Rcpp/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
  gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/usr/lib64/R/library/Rcpp/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 -fpic -fPIC -c datetime.c -o datetime.o
  gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/usr/lib64/R/library/Rcpp/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 -fpic -fPIC -c period.c -o period.o
  gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/usr/lib64/R/library/Rcpp/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 -fpic -fPIC -c tparse.c -o tparse.o
  tparse.c: In function ‘C_parse_dt’:
  tparse.c:62: warning: ‘oYEAR’ may be used uninitialized in this function
  tparse.c:62: warning: ‘oMONTH’ may be used uninitialized in this function
  tparse.c:62: warning: ‘oDAY’ may be used uninitialized in this function
  tparse.c:62: warning: ‘oHOUR’ may be used uninitialized in this function
  tparse.c:62: warning: ‘oMIN’ may be used uninitialized in this function
  tparse.c:290: warning: ‘is_leap’ may be used uninitialized in this function
  g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/usr/lib64/R/library/Rcpp/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 update.cpp -o update.o
  In file included from ./cctz/include/civil_time.h:18,
  from update.cpp:2:
  ./cctz/include/civil_time_detail.h:37: error: expected nested-name-specifier before ‘year_t’
  ./cctz/include/civil_time_detail.h:37: error: ‘year_t’ has not been declared
  ./cctz/include/civil_time_detail.h:37: error: expected ‘;’ before ‘=’ token
  ./cctz/include/civil_time_detail.h:37: error: expected unqualified-id before ‘=’ token
  ./cctz/include/civil_time_detail.h:41: error: expected nested-name-specifier before ‘diff_t’
  ./cctz/include/civil_time_detail.h:41: error: ‘diff_t’ has not been declared
  ./cctz/include/civil_time_detail.h:41: error: expected ‘;’ before ‘=’ token
  ./cctz/include/civil_time_detail.h:41: error: expected unqualified-id before ‘=’ token
  ./cctz/include/civil_time_detail.h:46: error: expected nested-name-specifier before ‘month_t’
  ./cctz/include/civil_time_detail.h:46: error: ‘month_t’ has not been declared
  ./cctz/include/civil_time_detail.h:46: error: expected ‘;’ before ‘=’ token
  ./cctz/include/civil_time_detail.h:46: error: expected unqualified-id before ‘=’ token
  ./cctz/include/civil_time_detail.h:47: error: expected nested-name-specifier before ‘day_t’
  ./cctz/include/civil_time_detail.h:47: error: ‘day_t’ has not been declared
  ./cctz/include/civil_time_detail.h:47: error: expected ‘;’ before ‘=’ token
  ./cctz/include/civil_time_detail.h:47: error: expected unqualified-id before ‘=’ token
  ./cctz/include/civil_time_detail.h:48: error: expected nested-name-specifier before ‘hour_t’
  ./cctz/include/civil_time_detail.h:48: error: ‘hour_t’ has not been declared
  ./cctz/include/civil_time_detail.h:48: error: expected ‘;’ before ‘=’ token
  ./cctz/include/civil_time_detail.h:48: error: expected unqualified-id before ‘=’ token
  ./cctz/include/civil_time_detail.h:49: error: expected nested-name-specifier before ‘minute_t’
  ./cctz/include/civil_time_detail.h:49: error: ‘minute_t’ has not been declared
  ./cctz/include/civil_time_detail.h:49: error: expected ‘;’ before ‘=’ token
  ./cctz/include/civil_time_detail.h:49: error: expected unqualified-id before ‘=’ token
  ./cctz/include/civil_time_detail.h:50: error: expected nested-name-specifier before ‘second_t’
  ./cctz/include/civil_time_detail.h:50: error: ‘second_t’ has not been declared
  ./cctz/include/civil_time_detail.h:50: error: expected ‘;’ before ‘=’ token
  ./cctz/include/civil_time_detail.h:50: error: expected unqualified-id before ‘=’ token
  ./cctz/include/civil_time_detail.h:54: error: expected ‘)’ before ‘year’
  ./cctz/include/civil_time_detail.h:78: error: ‘cctz::detail::impl::is_leap_year’ declared as an ‘inline’ variable
  ./cctz/include/civil_time_detail.h:78: error: ‘year_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:78: error: expected ‘,’ or ‘;’ before ‘noexcept’
  ./cctz/include/civil_time_detail.h:81: error: ‘cctz::detail::impl::year_index’ declared as an ‘inline’ variable
  ./cctz/include/civil_time_detail.h:81: error: ‘year_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:81: error: ‘month_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:81: error: initializer expression list treated as compound expression
  ./cctz/include/civil_time_detail.h:81: error: expected ‘,’ or ‘;’ before ‘noexcept’
  ./cctz/include/civil_time_detail.h:84: error: ‘cctz::detail::impl::days_per_century’ declared as an ‘inline’ variable
  ./cctz/include/civil_time_detail.h:84: error: ‘year_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:84: error: ‘month_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:84: error: initializer expression list treated as compound expression
  ./cctz/include/civil_time_detail.h:84: error: expected ‘,’ or ‘;’ before ‘noexcept’
  ./cctz/include/civil_time_detail.h:88: error: ‘cctz::detail::impl::days_per_4years’ declared as an ‘inline’ variable
  ./cctz/include/civil_time_detail.h:88: error: ‘year_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:88: error: ‘month_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:88: error: initializer expression list treated as compound expression
  ./cctz/include/civil_time_detail.h:88: error: expected ‘,’ or ‘;’ before ‘noexcept’
  ./cctz/include/civil_time_detail.h:92: error: ‘cctz::detail::impl::days_per_year’ declared as an ‘inline’ variable
  ./cctz/include/civil_time_detail.h:92: error: ‘year_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:92: error: ‘month_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:92: error: initializer expression list treated as compound expression
  ./cctz/include/civil_time_detail.h:92: error: expected ‘,’ or ‘;’ before ‘noexcept’
  ./cctz/include/civil_time_detail.h:95: error: ‘cctz::detail::impl::days_per_month’ declared as an ‘inline’ variable
  ./cctz/include/civil_time_detail.h:95: error: ‘year_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:95: error: ‘month_t’ was not declared in this scope
  ./cctz/include/civil_time_detail.h:95: error: initializer expression list treated as compound expression
  ./cctz/include/civil_time_detail.h:95: error: expected ‘,’ or ‘;’ before ‘noexcept’
  update.cpp:371: error: expected ‘}’ at end of input
  update.cpp:371: error: expected ‘}’ at end of input
  update.cpp:371: error: expected ‘}’ at end of input
  make: *** [update.o] Error 1
  ERROR: compilation failed for package ‘lubridate’
• removing ‘/usr/lib64/R/library/lubridate’

The downloaded source packages are in
‘/tmp/RtmpZAQIGJ/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("lubridate") :
installation of package ‘lubridate’ had non-zero exit status

[vspinu]

Well, I guess it's an outdated gcc compiler which is to blame. We need C++11 as CCTZ requires that. So the obvious options are

• update gcc if you can
• install lubridate 1.6 like devtools::install_version("lubridate", "1.6.0"). Not recommended as there a couple of severe bugs there.
• install dev version just before CCTZ devtools::install_github("tidyverse/lubridate@before-CCTZ")

Please let me know if any of the above worked for you.

Sorry about this but there is no way I am going back on CCTZ. It would be close to imposible to improve on time-zone manipulation and date-time updates without it.

[arnonerba]

Aha, another issue that can be blamed on RHEL 6's outdated set of system tools (it is gcc version 4.4.7). I'll see if I can update gcc; otherwise, I'll roll back to 1.6.0. Thanks for the help!

[c2b2pss]

@arnonerba : How did you update system tools? I do not have root permission and I need to update gcc. Will RHEL ever get with the program ???? frustrating

Thanks in advance.

[arnonerba]

@c2b2pss Unfortunately, I couldn't find a good solution to update gcc on RHEL 6 so I just rolled back lubridate. I doubt RHEL 6 will get a newer version of gcc, but RHEL 7 and CentOS 7 both include updated development tools.

[jpearl01]

I was able to download and compile a newer version of gcc on Centos 6. After adding these lines to the ~/.R/Makevars file:

CC=/opt/gcc_4.9.1/rtf/bin/gcc -std=gnu99
CXX1X=/opt/gcc_4.9.1/rtf/bin/g++

It successfully compiled using the newer version - unfortunately R doesn't correctly load the library:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/R/R-3.3.3/library/lubridate/libs/lubridate.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /opt/R/R-3.3.3/library/lubridate/libs/lubridate.so)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/R/R-3.3.3/library/lubridate’

And changing the LD_LIBRARY_PATH:
$ LD_LIBRARY_PATH="/opt/gcc_4.9.1/rtf/lib64/:$LD_LIBRARY_PATH"
(which I kind of don't want to do - would rather have something in the Makevars file) doesn't work either, though I do get a new error:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/R/R-3.3.3/library/lubridate/libs/lubridate.so':
  /opt/R/R-3.3.3/library/lubridate/libs/lubridate.so: undefined symbol: _ZN4cctz14load_time_zoneERKSsPNS_9time_zoneE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/R/R-3.3.3/library/lubridate’

I don't suppose there would be an easy fix for this?

[vspinu]

That symbol comes from the CCTZ library which suggests that linker couldn't find it in the lubridate.so archive. So either something went wrong during the compilation or linker looks at a wrong file. I occasionally see such errors during the development due to stale object files but restarting the session and re-installing from scratch always helps.

Regarding LD_LIBRARY_PATH you might be able to set it in .Renvioron file.

[jpearl01]

Hmm. I added the additional path to LD_LIBRARY_PATH in /opt/R/R-3.3.3/etc/ldpaths and that does get rid of the GLIBC error, but not the undefined symbol: _ZN4cctz14load_time_zoneERKSsPNS_9time_zoneE

gcc 4.9.1 should be a late enough version to be able to compile this, right?

[vspinu]

yes. 4.9.1 should be just fine. It's the linker problem, it somehow misses the symbol in the archive or R picks wrong archive. This is what I see on my machine:

~$ locate lubridate.so
/home/vspinu/.lib/R/lubridate/libs/lubridate.so
/store/Dropbox/dev/lubridate/src/lubridate.so
~$ nm -gC /store/Dropbox/dev/lubridate/src/lubridate.so  | grep load_time_zone
0000000000020720 T cctz::load_time_zone(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, cctz::time_zone*)
~$ nm -g /store/Dropbox/dev/lubridate/src/lubridate.so  | grep load_time_zone
0000000000020720 T _ZN4cctz14load_time_zoneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_9time_zoneE

[sckinta]

Any solution for undefined symbol: _ZNK4cctz9time_zone6lookupERKNS_6detail10civil_timeINS1_10second_tagEEE on RHEL 6 so far?