Unable to install curl package on centos6

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1

[root@ver1 user1]# /opt/vertica/R/bin/R CMD INSTALL /software/vertica_package/TTR_0.23-6.tar.gz

  • installing to library ‘/opt/vertica/R/library’
    ERROR: dependency ‘curl’ is not available for package ‘TTR’
  • removing ‘/opt/vertica/R/library/TTR’
    [root@ver1 user1]# ts CMD INSTALL /software/vertica_package/curl_4.3.tar.gz
  • installing to library ‘/opt/vertica/R/library’
  • installing source package ‘curl’ ...
    ** package ‘curl’ successfully unpacked and MD5 sums checked
    Found pkg-config cflags and libs!
    Using PKG_CFLAGS=
    Using PKG_LIBS=-lcurl
    ** libs
    rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c callbacks.c -o callbacks.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c curl.c -o curl.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c download.c -o download.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c escape.c -o escape.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c fetch.c -o fetch.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c form.c -o form.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c getdate.c -o getdate.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c handle.c -o handle.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c ieproxy.c -o ieproxy.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c init.c -o init.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c interrupt.c -o interrupt.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c multi.c -o multi.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c nslookup.c -o nslookup.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c reflist.c -o reflist.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c split.c -o split.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c ssl.c -o ssl.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c typechecking.c -o typechecking.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c utils.c -o utils.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c version.c -o version.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c winidn.c -o winidn.o
    gcc -std=gnu99 -I"/opt/vertica/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/include -I/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/bzip2/bzip2-1.0.6 -c writer.c -o writer.o
    gcc -std=gnu99 -shared -L/opt/vertica/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-rpath,$ORIGIN:$ORIGIN/../../lib,-z,origin -L/data/qb_workspaces/jenkins2/ReleaseBuilds/Grader/REL-9_2_1-x_grader/build/third-party/install/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/opt/vertica/R/lib -lR
    installing to /opt/vertica/R/library/curl/libs
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    Error: package or namespace load failed for ‘curl’ in dyn.load(file, DLLpath = DLLpath, ...):
    unable to load shared object '/opt/vertica/R/library/curl/libs/curl.so':
    /usr/lib64/libssh2.so.1: symbol EVP_cast5_cbc, version libcrypto.so.10 not defined in file libcrypto.so.10 with link time reference
    Error: loading failed
    Execution halted
    ERROR: loading failed
  • removing ‘/opt/vertica/R/library/curl’
2

indicates a system library dependency problem that must be resolved before the R packages that depend on it can compile. Something like

yum install -y openssl-devel

may be needed to fix this, but I have no Centos installation against which to test.

3

Hi @technocrat

Thanks for the response, I tried your suggestion but no luck. Still i'm facing the same issue.

4

What is the output of ldd /usr/lib64/libssh2.so.1? Have you installed SSH or OpenSSL from a non-standard repository?

1 Like
5

Hi @rstub

What is the output of ldd /usr/lib64/libssh2.so.1 ?
[root@ver1]$ ldd /usr/lib64/libssh2.so.1
linux-vdso.so.1 => (0x00007ffe4351e000)
libssl.so.10 => /usr/lib64/libssl.so.10 (0x00007fbcf324d000)
libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00007fbcf2e68000)
libz.so.1 => /lib64/libz.so.1 (0x0000003805000000)
libc.so.6 => /lib64/libc.so.6 (0x0000003803c00000)
libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x000000380e400000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x000000380f000000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x000000380c000000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x000000380ec00000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003804400000)
/lib64/ld-linux-x86-64.so.2 (0x0000558dbfe59000)
libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x000000380e800000)
libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x000000380e000000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x0000003808400000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003804000000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x0000003805400000)
Have you installed SSH or OpenSSL from a non-standard repository?
No

6

Very strange. And which compiler are you using (gcc --version)?

1 Like
7

Hi @rstub

[root@ver1]# gcc --version

gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)

Copyright (C) 2010 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.

8

This looks all the way it should be. I am out of ideas, in particular since I have no easy way to test this myself (the Docker images for CentOS 6 give SEGV on my machine).

9

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