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error on redhat with lssh2 #195

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taylordm opened this issue Jan 14, 2023 · 3 comments
Open

error on redhat with lssh2 #195

taylordm opened this issue Jan 14, 2023 · 3 comments

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@taylordm
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Redhat has deprecated lssh2 in version 8. Any workaround to install gert with that limitation?

Operating System: Red Hat Enterprise Linux 8.6 (Ootpa)
CPE OS Name: cpe:/o:redhat:enterprise_linux:8::baseos
Kernel: Linux 4.18.0-372.26.1.el8_6.x86_64

`install.packages("gert", repos = c(ropensci = 'https://ropensci.r-universe.dev', CRAN = 'https://cloud.r-project.org'))
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)

trying URL 'https://ropensci.r-universe.dev/src/contrib/gert_1.9.2.tar.gz'

Content type 'application/x-gzip' length 296424 bytes (289 KB)

downloaded 289 KB

  • installing source package ‘gert’ ...
    ** using staged installation
    Error in curl::curl_download("https://autobrew.github.io/archive/x86_64_linux/libgit2-1.4.2-x86_64_linux.tar.gz", :
    OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to autobrew.github.io:443
    Execution halted
    tar (child): bundle.tar.gz: Cannot open: No such file or directory
    tar (child): Error is not recoverable: exiting now
    tar: Child returned status 2
    tar: Error is not recoverable: exiting now
    Using static libgit2 for Linux x86_64
    Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include
    Using PKG_LIBS=-L/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/lib -lgit2 -lrt -lpthread -lssh2 -lssl -lcrypto -ldl
    Configuration OK!
    ** libs
    rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c branch.c -o branch.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c clone.c -o clone.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c commit.c -o commit.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c config.c -o config.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c conflicts.c -o conflicts.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c files.c -o files.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c init.c -o init.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c merge.c -o merge.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rebase.c -o rebase.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c stash.c -o stash.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c submodules.c -o submodules.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c tag.c -o tag.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils.c -o utils.o
    gcc -I"/usr/include/R" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c version.c -o version.o
    gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o gert.so branch.o clone.o commit.o config.o conflicts.o files.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o -L/tmp/RtmpyC9to7/R.INSTALL21d4f12c99c669/gert/libgit2-1.4.2-x86_64_linux/lib -lgit2 -lrt -lpthread -lssh2 -lssl -lcrypto -ldl -L/usr/lib64/R/lib -lR
    /usr/bin/ld: cannot find -lssh2
    collect2: error: ld returned 1 exit status
    make: *** [/usr/share/R/make/shlib.mk:10: gert.so] Error 1
    ERROR: compilation failed for package ‘gert’
  • removing ‘/usr/lib64/R/library/gert’
  • restoring previous ‘/usr/lib64/R/library/gert’
    Warning in install.packages :
    installation of package ‘gert’ had non-zero exit status`
@jeroen
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jeroen commented Jan 14, 2023

Well the workaround is already in place: it is trying to download a static libgit2 from https://autobrew.github.io/archive/x86_64_linux/libgit2-1.4.2-x86_64_linux.tar.gz but it seems you don't have an internet connection?

@taylordm
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taylordm commented Jan 14, 2023 via email

@jeroen
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jeroen commented Jan 14, 2023 •
edited

Yes you can use libgit2-devel from your system. But the drawback is that it is an older version of libgit2 and cloning from git-ssh remotes wont work because as you indicate yourself, redhat does not have libssh2.

But if you want this you can force this by setting the envvar USE_SYSTEM_LIBGIT2.

Sys.setenv(USE_SYSTEM_LIBGIT2=1)
install.packages("gert", repos = 'https://ropensci.r-universe.dev')

I think the error in your first post was a temporary internet problem on your side...

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@jeroen @taylordm