Still Cairo installation issue - r

Question

I also faced an error during Cairo library installation in R. Please, see the messages below.
I get this error:
> install.packages('Cairo')
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 86982 100 86982 0 0 389k 0 --:--:-- --:--:-- --:--:-- 389k
* installing *source* package ‘Cairo’ ...
** package ‘Cairo’ successfully unpacked and MD5 sums checked
checking for gcc... x86_64-conda_cos6-linux-gnu-cc
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 x86_64-conda_cos6-linux-gnu-cc accepts -g... yes
checking for x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-conda_cos6-linux-gnu-cc -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/wait.h that is POSIX.1 compatible... 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 for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pkg-config... /usr/bin/pkg-config
checking whether pkg-config knows about cairo... yes
checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender
configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12
checking if R was compiled with the RConn patch... no
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
checking for ATS font support in Cairo... no
configure: CAIRO_LIBS=-lfreetype -lz -lpng12 -lz -lcairo -lXext -lXrender -lX11
checking for library containing deflate... no
checking whether Cairo programs can be compiled... configure: error: Cannot compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’
* removing ‘/home/ubuntu/anaconda3/lib/R/library/Cairo’
The downloaded source packages are in
‘/tmp/RtmpAuSLZy/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("Cairo") :
installation of package ‘Cairo’ had non-zero exit status
While session info gives this:
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /home/ubuntu/anaconda3/lib/R/lib/libRblas.so
LAPACK: /home/ubuntu/anaconda3/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RevoUtils_10.0.8
loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3
And capabilities shows I have Cairo available.
> capabilities()
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE TRUE TRUE TRUE TRUE
NLS profmem cairo ICU long.double libcurl
TRUE TRUE TRUE TRUE TRUE TRUE
I believe I read all the corresponding topics and librairo2-dev is already installed:
libcairo2-dev is already the newest version (1.14.6-1).
And, I believe, the .log file:
## --------- ##
## Platform. ##
## --------- ##
hostname = ip-172-31-30-74
uname -m = x86_64
uname -r = 4.4.0-1069-aws
uname -s = Linux
uname -v = #79-Ubuntu SMP Mon Sep 24 15:01:41 UTC 2018
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /home/ubuntu/bin
PATH: /home/ubuntu/.local/bin
PATH: /home/ubuntu/anaconda3/bin
PATH: /home/ubuntu/software/sratoolkit.2.9.0-ubuntu64/bin
PATH: /home/ubuntu/anaconda2/bin
PATH: /home/ubuntu/chenlab_v2/pipeline/bulk_rna_seq/code
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /usr/local/games
PATH: /snap/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2155: checking for gcc
configure:2171: found /home/ubuntu/anaconda3/bin/gcc
configure:2182: result: gcc
configure:2411: checking for C compiler version
configure:2420: gcc --version >&5
gcc (crosstool-NG fa8859cb) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:2431: $? = 0
configure:2420: gcc -v >&5
Reading specs from /home/ubuntu/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/specs
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/home/ubuntu/anaconda3/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/lto-wrapper
Target: x86_64-conda_cos6-linux-gnu
Configured with: /opt/conda/conda-bld/compilers_linux-64_1520532893746/work/.build/src/gcc-7.2.0/configure --build=x86_64-build_pc-linux-gnu --host=x86_64-build_pc-linux-gnu --tar
get=x86_64-conda_cos6-linux-gnu --prefix=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/gcc_built --with-sysroot=/opt/conda/conda-bld/compilers_linux-64_1520532893746/
work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-languages=c,c++,fortran,objc,obj-c++ --with-pkgversion='crosstool-NG fa8859cb' --enable-__cxa_atexit --disable-libmudfl
ap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-libsanitizer --enable-libmpx --with-gmp=/opt/conda/conda-bld/compilers_linux-64_152
0532893746/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpfr=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/.build/x86_64-conda_cos6-linux-gnu/buildtools
--with-mpc=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-isl=/opt/conda/conda-bld/compilers_linux-64_152053289374
6/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --enable-lto --enable-threads=posix --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-multilib --
with-local-prefix=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-long-long --enable-default-pie
Thread model: posix
gcc version 7.2.0 (crosstool-NG fa8859cb)
configure:2431: $? = 0
configure:2420: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2431: $? = 1
configure:2420: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc: fatal error: no input files
compilation terminated.
configure:2431: $? = 1
configure:2451: checking whether the C compiler works
configure:2473: gcc -L/home/ubuntu/anaconda3/lib conftest.c >&5
configure:2477: $? = 0
configure:2525: result: yes
configure:2528: checking for C compiler default output file name
configure:2530: result: a.out
configure:2536: checking for suffix of executables
configure:2543: gcc -o conftest -L/home/ubuntu/anaconda3/lib conftest.c >&5
configure:2547: $? = 0
configure:2569: result:
configure:2591: checking whether we are cross compiling
configure:2599: gcc -o conftest -L/home/ubuntu/anaconda3/lib conftest.c >&5
configure:2603: $? = 0
configure:2610: ./conftest
configure:2614: $? = 0
configure:2629: result: no
configure:2634: checking for suffix of object files
configure:2656: gcc -c conftest.c >&5
configure:2660: $? = 0
configure:2681: result: o
configure:2685: checking whether we are using the GNU C compiler
configure:2704: gcc -c conftest.c >&5
configure:2704: $? = 0
configure:2713: result: yes
configure:2722: checking whether gcc accepts -g
configure:2742: gcc -c -g conftest.c >&5
configure:2742: $? = 0
configure:2783: result: yes
configure:2800: checking for gcc option to accept ISO C89
configure:2863: gcc -c -g -O2 conftest.c >&5
configure:2863: $? = 0
configure:2876: result: none needed
configure:2897: checking for gzeof in -lz
configure:2922: gcc -o conftest -g -O2 -L/home/ubuntu/anaconda3/lib conftest.c -lz >&5
/home/ubuntu/anaconda3/lib/libz.so: undefined reference to `memcpy#GLIBC_2.14'
collect2: error: ld returned 1 exit status
configure:2922: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h. */
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char gzeof ();
| int
| main ()
| {
| return gzeof ();
| ;
| return 0;
| }
configure:2931: result: yes
configure:2949: checking how to run the C preprocessor
configure:2980: gcc -E conftest.c
configure:2980: $? = 0
configure:2994: gcc -E conftest.c
conftest.c:10:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:2994: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:3019: result: gcc -E
configure:3039: gcc -E conftest.c
configure:3039: $? = 0
configure:3053: gcc -E conftest.c
conftest.c:10:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:3053: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:3082: checking for grep that handles long lines and -e
configure:3140: result: /bin/grep
configure:3145: checking for egrep
configure:3207: result: /bin/grep -E
configure:3212: checking for ANSI C header files
configure:3232: gcc -c -g -O2 conftest.c >&5
configure:3232: $? = 0
configure:3305: gcc -o conftest -g -O2 -L/home/ubuntu/anaconda3/lib conftest.c -lz >&5
/home/ubuntu/anaconda3/lib/libz.so: undefined reference to `memcpy#GLIBC_2.14'
collect2: error: ld returned 1 exit status
configure:3305: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| /* end confdefs.h. */
| #include <ctype.h>
| #include <stdlib.h>
| #if ((' ' & 0x0FF) == 0x020)
| # define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
| # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
| #else
| # define ISLOWER(c) (('a' <= (c) && (c) <= 'i') || ('j' <= (c) && (c) <= 'r') || ('s' <= (c) && (c) <= 'z'))
| # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
| #endif
|
| #define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
| int
| main ()
| {
| int i;
| for (i = 0; i < 256; i++)
| if (XOR (islower (i), ISLOWER (i))
| || toupper (i) != TOUPPER (i))
| return 2;
| return 0;
| }
configure:3316: result: no
configure:3329: checking for sys/types.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for sys/stat.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for stdlib.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for string.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for memory.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for strings.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for inttypes.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for stdint.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for unistd.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3345: checking size of unsigned long
configure:3350: gcc -o conftest -g -O2 -L/home/ubuntu/anaconda3/lib conftest.c -lz >&5
/home/ubuntu/anaconda3/lib/libz.so: undefined reference to `memcpy#GLIBC_2.14'
collect2: error: ld returned 1 exit status
configure:3350: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| static long int longval () { return (long int) (sizeof (unsigned long)); }
| static unsigned long int ulongval () { return (long int) (sizeof (unsigned long)); }
| #include <stdio.h>
| #include <stdlib.h>
| int
| main ()
| {
|
| FILE *f = fopen ("conftest.val", "w");
| if (! f)
| return 1;
| if (((long int) (sizeof (unsigned long))) < 0)
| {
| long int i = longval ();
| if (i != ((long int) (sizeof (unsigned long))))
| return 1;
| fprintf (f, "%ld", i);
| }
| else
| {
| unsigned long int i = ulongval ();
| if (i != ((long int) (sizeof (unsigned long))))
| return 1;
| fprintf (f, "%lu", i);
| }
| /* Do not output a trailing newline, as this causes \r\n confusion
| on some platforms. */
| return ferror (f) || fclose (f) != 0;
|
| ;
| return 0;
| }
configure:3364: result: 0
configure:3527: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by config.status, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on ip-172-31-30-74
config.status:723: creating src/Makevars
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=-L/home/ubuntu/anaconda3/lib
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=no
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_lib_z_gzeof=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_sizeof_unsigned_long=0
## ----------------- ##
## Output variables. ##
## ----------------- ##
CC='gcc'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
DEFS='-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DHAVE_SYS_TYPES_H=1 -DHAVE
_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=0'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
LDFLAGS='-L/home/ubuntu/anaconda3/lib'
LIBOBJS=''
LIBS='-lz '
LTLIBOBJS=''
OBJEXT='o'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_URL=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
SHELL='/bin/bash'
ac_ct_CC='gcc'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define PACKAGE_STRING ""
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define HAVE_LIBZ 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define SIZEOF_UNSIGNED_LONG 0
configure: exit 0
I would greatly appreciate if someone will be able to help. Thank you in advance.