Hi guys,
I can't install tidyverse because i'm not able to install lubridate package first. I tried to upgrade my C compiler to 4.9.3 but nothing happen.
My server is Centos 6. 64
> install.packages("lubridate")
Installing package into ‘/home/admin/R/x86_64-redhat-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
essai de l'URL 'https://cran.rstudio.com/src/contrib/lubridate_1.7.3.tar.gz'
Content type 'application/x-gzip' length 447719 bytes (437 KB)
==================================================
downloaded 437 KB
* installing *source* package ‘lubridate’ ...
** package ‘lubridate’ correctement décompressé et sommes MD5 vérifiées
** libs
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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:338:26: attention : ‘oMIN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(oMIN)[i] = M;
^
tparse.c:337:27: attention : ‘oHOUR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(oHOUR)[i] = H;
^
tparse.c:336:26: attention : ‘oDAY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(oDAY)[i] = d;
^
tparse.c:335:28: attention : ‘oMONTH’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(oMONTH)[i] = m - 1;
^
tparse.c:334:27: attention : ‘oYEAR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(oYEAR)[i] = y - 1900;
^
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 utils.c -o utils.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 cctz/src/time_zone_fixed.cc -o cctz/src/time_zone_fixed.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 cctz/src/time_zone_if.cc -o cctz/src/time_zone_if.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 cctz/src/time_zone_impl.cc -o cctz/src/time_zone_impl.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 cctz/src/time_zone_info.cc -o cctz/src/time_zone_info.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 cctz/src/time_zone_libc.cc -o cctz/src/time_zone_libc.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 cctz/src/time_zone_lookup.cc -o cctz/src/time_zone_lookup.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/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 cctz/src/time_zone_posix.cc -o cctz/src/time_zone_posix.o
ar rcs libcctz.a ./cctz/src/time_zone_fixed.o ./cctz/src/time_zone_if.o ./cctz/src/time_zone_impl.o ./cctz/src/time_zone_info.o ./cctz/src/time_zone_libc.o ./cctz/src/time_zone_lookup.o ./cctz/src/time_zone_posix.o
g++ -m64 -std=gnu++0x -shared -L/usr/lib64/R/lib -o lubridate.so RcppExports.o datetime.o period.o tparse.o update.o utils.o -L. -lcctz -L/usr/lib64/R/lib -lR
installing to /home/admin/R/x86_64-redhat-linux-gnu-library/3.4/lubridate/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package ‘lubridate’
finding HTML links ... fini
DateCoercion html
DateTimeUpdate html
Deprecated html
Duration-class html
Interval-class html
Period-class html
Timespan-class html
am html
as.duration html
as.interval html
as.period html
as_date html
date html
date_decimal html
day html
days_in_month html
decimal_date html
dst html
duration html
fit_to_timeline html
force_tz html
guess_formats html
hidden_aliases html
hms html
hour html
interval html
is.Date html
is.POSIXt html
is.difftime html
is.instant html
is.timespan html
lakers html
leap_year html
local_time html
lubridate-package html
make_datetime html
Rd warning: /tmp/Rtmpp2bNtP/R.INSTALL1a9d4dd42dcf/lubridate/man/make_datetime.Rd:30: missing file link ‘ISOdate’
make_difftime html
minute html
month html
mplus html
now html
origin html
parse_date_time html
period html
period_to_seconds html
pretty_dates html
quarter html
reclass_date html
reclass_timespan html
rollback html
round_date html
Rd warning: /tmp/Rtmpp2bNtP/R.INSTALL1a9d4dd42dcf/lubridate/man/round_date.Rd:50: missing file link ‘round’
Rd warning: /tmp/Rtmpp2bNtP/R.INSTALL1a9d4dd42dcf/lubridate/man/round_date.Rd:147: missing file link ‘round’
second html
stamp html
time_length html
timespan html
today html
tz html
week html
with_tz html
within-interval html
year html
ymd html
ymd_hms html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘lubridate’ in dyn.load(file, DLLpath = DLLpath, ...):
impossible de charger l'objet partagé '/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/lubridate/libs/lubridate.so':
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /home/admin/R/x86_64-redhat-linux-gnu-library/3.4/lubridate/libs/lubridate.so)
Erreur : le chargement a échoué
Exécution arrêtée
ERROR: loading failed
* removing ‘/home/admin/R/x86_64-redhat-linux-gnu-library/3.4/lubridate’
Warning in install.packages :
installation of package ‘lubridate’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpgBPpgF/downloaded_packages’
Please help me to understand all requirements and how to resolve this issue
Best,
Saber
Could it be that you installed gcc-4.9 but left alone libstdc++? Or some path messup?
Judging from this page gcc-4.9 needs GLIBCXX_3.4.2 on your system.
This is what I have on my ubuntu machine (found here):
~$ /sbin/ldconfig -p | grep stdc++
libstdc++.so.6 (libc6,x32) => /usr/libx32/libstdc++.so.6
libstdc++.so.6 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
libstdc++.so.6 (libc6) => /usr/lib/i386-linux-gnu/libstdc++.so.6
libstdc++.so.6 (libc6) => /usr/lib32/libstdc++.so.6
~$ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep LIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_DEBUG_MESSAGE_LENGTH
Thank you @vspinu you helped me learn something new and resolve this issue.
sudo yum install libmpc-devel mpfr-devel gmp-devel
wget https://ftp.gnu.org/gnu/gcc/gcc-4.9.0/gcc-4.9.0.tar.bz2
tar xvfj gcc-4.9.0.tar.bz2
cd gcc-4.9.0
./configure --disable-multilib --enable-languages=c,c++
make -j 4
make install
Apply the fix above still getting error. What should I do ?@saberbouabid @vspinu
install.packages('tidyverse')
Installing package into ‘/home/sakshi/R/x86_64-redhat-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependency ‘lubridate’
trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.7.4.tar.gz'
Content type 'application/x-gzip' length 449850 bytes (439 KB)
downloaded 439 KB
trying URL 'https://cran.rstudio.com/src/contrib/tidyverse_1.2.1.tar.gz'
Content type 'application/x-gzip' length 61647 bytes (60 KB)
downloaded 60 KB
The downloaded source packages are in
‘/tmp/RtmpyvCw8v/downloaded_packages’
Most helpful comment
Could it be that you installed gcc-4.9 but left alone libstdc++? Or some path messup?
Judging from this page gcc-4.9 needs GLIBCXX_3.4.2 on your system.
This is what I have on my ubuntu machine (found here):