Question: (Closed) Problems installing devtools in R
0
gravatar for sgmiriuka
22 months ago by
sgmiriuka0
sgmiriuka0 wrote:

Hi there,

I am having many troubles installing devtools in R (Ubuntu 16-04). No problems in OSX, but not sure why I can't get anywhere in Ubuntu. These is the error log. No idea why I get so many error when trying to install dependencies, which in fact I installed. I understand that it can't find them, but no idea why

Yes, I am a begginer in all these... Thanks in advance!!


* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rawmatch.c -o rawmatch.o

gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’

/usr/lib/R/etc/Makeconf:159: recipe for target 'rawmatch.o' failed
make: *** [rawmatch.o] Error 1

ERROR: compilation failed for package ‘mime’

* removing ‘/home/sgmiriuka/R/x86_64-pc-linux-gnu-library/3.4/mime’

Warning in install.packages :
  installation of package ‘mime’ had non-zero exit status

* 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

------------------------- ANTICONF ERROR ---------------------------

Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)

If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

--------------------------------------------------------------------

ERROR: configuration failed for package ‘curl’
* removing ‘/home/sgmiriuka/R/x86_64-pc-linux-gnu-library/3.4/curl’

Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status

* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto

------------------------- ANTICONF ERROR ---------------------------

Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl@1.1 (Mac OSX)

If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

--------------------------------------------------------------------

ERROR: configuration failed for package ‘openssl’

* removing ‘/home/sgmiriuka/R/x86_64-pc-linux-gnu-library/3.4/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status

* installing *source* package ‘digest’ ...

** package ‘digest’ successfully unpacked and MD5 sums checked

** libs

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c aes.c -o aes.o

gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’

/usr/lib/R/etc/Makeconf:159: recipe for target 'aes.o' failed
make: *** [aes.o] Error 1

ERROR: compilation failed for package ‘digest’

* removing ‘/home/sgmiriuka/R/x86_64-pc-linux-gnu-library/3.4/digest’

Warning in install.packages :

  installation of package ‘digest’ had non-zero exit status

* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** libs

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c base64.c -o base64.o

gcc: error: unrecognized command line option ‘-fstack-protector-strong’

gcc: error: unrecognized command line option ‘-Wdate-time’

/usr/lib/R/etc/Makeconf:159: recipe for target 'base64.o' failed
make: *** [base64.o] Error 1

ERROR: compilation failed for package ‘jsonlite’
* removing ‘/home/sgmiriuka/R/x86_64-pc-linux-gnu-library/3.4/jsonlite’
Warning in install.packages :

  installation of package ‘jsonlite’ had non-zero exit status
R • 3.4k views
ADD COMMENTlink modified 10 months ago by RamRS20k • written 22 months ago by sgmiriuka0

gcc: error: unrecognized command line option

This could point to an obsolete version of gcc, at least a version that's too old for what you're trying to install. What is the output of gcc --version ?

ADD REPLYlink modified 22 months ago • written 22 months ago by Jean-Karim Heriche18k

Another error - and solution - is here:

Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) * csw: libcurl_dev (Solaris)

Solution: apt-get install libcurl4-openssl-dev

ADD REPLYlink written 22 months ago by h.mon24k

Hello sgmiriuka!

We believe that this post does not fit the main topic of this site.

I do not see a connection to bioinformatics in package devtools.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 22 months ago by Michael Dondrup45k

ok, understood.

just trying to install devtools as required by the new Tuxedo (hisat2, springtie, samtools, gffcompare, doi:10.1038/nprot.2016.095).

my apologize if I was wrong, looked like a bioinfo question in this context.

By the way, the two answers I got didn't solve the problem.

ADD REPLYlink written 22 months ago by sgmiriuka0
1

You might have a broken R install on your ubuntu system, that is going beyond what we can fix here and is likely affecting a lot of source packages, sorry.

Just google the first error: gcc: error: unrecognized command line option ‘-fstack-protector-strong’ gcc: error: unrecognized command line option ‘-Wdate-time’

ADD REPLYlink written 22 months ago by Michael Dondrup45k
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