Installation failed on CentOS7 with R 3.5.3

[ehenrion]

Hi there,

I am having trouble installing binless....

I am working on CentOS7 with R3.5.3 and tried the following command :
devtools::install_github("3DGenomes/binless/binless")

Everything seems to go quite smoothly during compilation, then....
Here is the end of the output :
`g++ -std=gnu++11 -shared -Linstall_path_of_R/lib64/R/lib -L/usr/local/lib64 -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -Linstall_path_of_R/lib64/R/lib -lR
installing to install_path_of_R/lib64/R/library/binless/libs
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package ‘binless’
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘binless’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object 'install_path_of_R/lib64/R/library/binless/libs/binless.so':
install_path_of_R/lib64/R/library/binless/libs/binless.so: undefined symbol: _ZN5boost9iostreams20file_descriptor_sinkC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt13_Ios_Openmode
Error: loading failed
Execution halted
ERROR: loading failed

• removing ‘install_path_of_R/lib64/R/library/binless’
  Error in i.p(...) :
  (converted from warning) installation of package ‘/gs/scratch/ehenrion/RtmpqcSM3H/filed9f577dd233/binless_0.15.0.tar.gz’ had non-zero exit status

`

Any help would be greatly appreciated !

Thanks so much,
Edouard

[yannickspill]

It seems like there's a problem with the boost libraries. Either they're not installed, or they're not loaded. I don't remember how you install a package in centos (`yum`? ). If it's installed maybe you use `module` to load and unload packages? In that case you should load boost prior to running R. You might get similar problems with other libraries. Check the readme for the list of package dependencies.

…

________________________________ From: ehenrion <notifications@github.com> Sent: Thursday, May 2, 2019 10:50:44 PM To: 3DGenomes/binless Cc: Subscribed Subject: [3DGenomes/binless] Installation failed on CentOS7 with R 3.5.3 (#8) Hi there, I am having trouble installing binless.... I am working on CentOS7 with R3.5.3 and tried the following command : devtools::install_github("3DGenomes/binless/binless") Everything seems to go quite smoothly during compilation, then.... Here is the end of the output : `... g++ -std=gnu++11 -shared -Linstall_path_of_R/lib64/R/lib -L/usr/local/lib64 -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -Linstall_path_of_R/lib64/R/lib -lR installing to install_path_of_R/lib64/R/library/binless/libs ** R ** byte-compile and prepare package for lazy loading ** help No man pages found in package ‘binless’ *** installing help indices ** building package indices ** testing if installed package can be loaded Error: package or namespace load failed for ‘binless’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object 'install_path_of_R/lib64/R/library/binless/libs/binless.so': install_path_of_R/lib64/R/library/binless/libs/binless.so: undefined symbol: _ZN5boost9iostreams20file_descriptor_sinkC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt13_Ios_Openmode Error: loading failed Execution halted ERROR: loading failed * removing ‘install_path_of_R/lib64/R/library/binless’ Error in i.p(...) : (converted from warning) installation of package ‘/gs/scratch/ehenrion/RtmpqcSM3H/filed9f577dd233/binless_0.15.0.tar.gz’ had non-zero exit status ` Any help would be greatly appreciated ! Thanks so much, Edouard — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#8>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AA455NPFFO53O4RFIGAHCZDPTNH2JANCNFSM4HKHXNLA>.

[ehenrion]

Hi,
Thanks a lot for your answer.
Boost libraries are installed already, with yum install boost and yum install boost-devel.
I indeed load a module prior to using R, so I'll check if system libraries are well loaded.
I think I installed all the dependencies but still, I'll also have a second look at the readme !
Thanks again, I'll let you know how it goes.
Ed

[ehenrion]

So...
I confirm all the dependencies (system libraries as well as R packages) are well installed...
I still have the same issue and don't know where to look anymore...
I'm surprised to have issues since binless has been developped on CentOS 7, as mentioned in the 'requirements' section of the readme...
By chance, would you have any other idea ?
Thanks
Edouard

[yannickspill]

Let's try a manual installation. Could you please open a fresh terminal, unpack the latest release source file, and type
module load the packages you need
env
R CMD INSTALL --preclean binless
And report the output of all above commands here

[david-castillo]

Hi,

There seems to be a problem linking to the boost libraries. You can check that the boost libraries are in their place by doing:

rpm -ql boost-devel

Verify also that the installed boost libraries are the 64bit libraries if your system is 64bits. Try to install

sudo yum install boost-devel.x86_64

Regards

David

[ehenrion]

Hi there !
Sorry for coming back to you that late...
I have been following another lead and I think I found the problem...

First to answer your questions :
I had the exact same error when trying the command R CMD INSTALL --preclean binless.
I also ensured to have the right boost libraries installed boost-devel.x86_64 and everything was good there too.

On my side, I tried to go the rough way by hunting for the undefined symbol _ZN5boost9iostreams20file_descriptor_sinkC1ERKNSt7__cxx1112basic_stringIcSt11char_traitIcESaIcEEEt13_Ios_Openmode

The boost libraries being installed in /usr/lib64/
I did the following :

-sh-4.2# cd /usr/lib64/
-sh-4.2# grep -R "_ZN5boost9iostreams20file_descriptor_sinkC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt13_Ios_Openmode" *

This unfortunately gave me no result...
This made me wonder if it was not a problem of version of the boost libraries...
What version did you use ?

On CentOS 7, the version of the boost libraries being 1.53.0

-sh-4.2# rpm -qa | grep boost-devel
boost-devel-1.53.0-27.el7.x86_64

I decided to install a newer version (1.66.0) as a module and went hunting again :

-sh-4.2# cd /path/of/my/boost-1.66.0
-sh-4.2# grep -R "_ZN5boost9iostreams20file_descriptor_sinkC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt13_Ios_Openmode" *
Binary file lib/libboost_iostreams.so.1.66.0 matches
Binary file lib/libboost_iostreams.so matches

Great !!! isn't it ?
But... (why is there always a 'but' ?...)
Even after loading my boost-1.66.0 module, I still have the same error... it seems R does not see the path I included by loading my module...

Here is what my module file does :

prepend-path     LD_LIBRARY_PATH      /path/of/my/boost-1.66.0/lib 
prepend-path     LIBRARY_PATH            /path/of/my/boost-1.66.0/lib 
prepend-path     CPATH                           /path/of/my/boost-1.66.0/include 
setenv                BOOST_ROOT              /path/of/my/boost-1.66.0/

Do you see anything missing ?

I feel like I am almost there.
Hopefully this will come to an end soon !

Regards,
Edouard

[david-castillo]

Hi,

Maybe the LD_LIBRARY_PATH is not properly passed to R.
Can you start an R session and do Sys.getenv(c("PATH", "LD_LIBRARY_PATH")) ?

You should see the path where the library is

Regards

David

[ehenrion]

Hi,

This is also what I thought but LD_LIBRARY_PATH is updated : the boost libraries folder is appended to LD_LIBRARY_PATH.

Here it the output of the command :

> Sys.getenv(c("PATH", "LD_LIBRARY_PATH"))
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   PATH 
"/path/of/my/installation/of/R/bin:
/opt/torque/x86_64/bin:/opt/moab/bin:
/usr/lib64/qt-3.3/bin:
/opt/moab/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:
/usr/sbin:/sbin:/usr/lpp/mmfs/bin:/sb/software/tools/scripts:/home/ehenrion/bin" 

LD_LIBRARY_PATH
"/path/of/my/installation/of/R/lib:/usr/local/lib64:/usr/local/lib/gcc/x86_64-pc-linux-gnu/8.3.0:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.41.x86_64/jre/lib/amd64/server:
path/of/my/boost-1.66.0/lib"

Regards,
Ed

[david-castillo]

Hi,
And downloading the source folder and installing it with install.packages(path_to_folder, repos = NULL, type="source") ?
Does it give the same error?

I'm also running out of ideas
Regards
David

[yannickspill]

Another question: how do you load R? Through rstudio, or in a shell, plain R ?
In some cases I had trouble installing packages from studio, but it did work from the bash using R CMD. Then once installed it would work in rstudio as well...

[ehenrion]

@yannickspill
I just edited my former answer for display purposes...

You should now be able to see the LD_LIBRARY_PATH value, the last entry being boost/lib .
Indeed, nothing related to Boost is added to PATH...

I use plain R, not Rstudio...

@david-castillo

Haha ! you are running out of idea too ! :)
I just tried the install.packages command and it ended up with the same error...

What version of Boost are you guys using ?
I will try to install binless on Ubuntu 16.04. I am pretty sure their version of Boost is newer than what we have on CentOS 7...

If I ever succeed to make it work on CentOS 7 (with or without the use of modules) I will let you guys know for sure.

Thanks a lot for you help !
I'll give you updates of my test on Ubuntu OS.

Regards,
Ed

[yannickspill]

Yes, let us know! This is indeed weird and I suspect this is related to module, since I developed it on a centos 7 machine without problems... I will check it out tomorrow to see how my environment paths look like

[david-castillo]

I'm also on centos 7. My boost libraries are 1.53.0 but I'm pretty sure the version of boost is not the problem.
If you are interested I also installed it under a conda environment. I can try to do a fresh install under conda and pass you the packages you need.

Regards

David

[ehenrion]

@yannickspill
Sure !!
My goal for now is to make it work : you know what it is... people are waiting after me...
But as soon as this is done, I will come back to CentOS 7 and try to make it work !
You are right, the modules definitely seem to be related to the problem...
I'll let you know how it goes.

@david-castillo
Yes, I would appreciate that !!
I will try with Ubuntu first, see how it goes.

Thanks again for your help and for your time !

Regards,
Ed

[yannickspill]

Here are a couple of things I could think of out of the top of my head. I don't use module btw. I have boost 1.53.0 headers in /usr/include/boost and compiled libraries in /usr/lib64/libboost_*

I think you don't need R to be aware of the location of boost libraries and headers. What matters, is that the C++ compiler does.

$ env
USER=yannick
LOGNAME=yannick
HOME=/home/yannick
PATH=/usr/local/texlive/2014/bin/x86_64-linux:/usr/lib64/qt-3.3/bin:/home/yannick/perl5/bin:/usr/local/bin/ncbi:/usr/lib64/mpich/bin:/usr/local/bin/kentUtils:/usr/lib64/python2.7/site-packages/gem/gembinaries:/usr/local/bin/fastqc:/usr/lib64/ccache:/usr/local/bin/bowtie2:/usr/local/bin:/usr/bin:/home/yannick/bin:/usr/local/sbin:/usr/sbin:/home/yannick/scripts
MAIL=/var/spool/mail/yannick
SHELL=/bin/zsh
SSH_CLIENT=192.168.103.156 53848 22
SSH_CONNECTION=192.168.103.156 53848 172.16.54.2 22
SSH_TTY=/dev/pts/0
TERM=xterm-256color
DISPLAY=localhost:10.0
SELINUX_ROLE_REQUESTED=
SELINUX_LEVEL_REQUESTED=
SELINUX_USE_CURRENT_RANGE=
XDG_SESSION_ID=2277
XDG_RUNTIME_DIR=/run/user/1000
SHLVL=1
PWD=/home/yannick/simulations/cs_norm
OLDPWD=/home/yannick
HISTCONTROL=ignoredups
HOSTNAME=panzer.pcb.ub.es
HISTSIZE=50000
KDEDIRS=/usr
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
LANG=en_US.UTF-8
LESSOPEN=||/usr/bin/lesspipe.sh %s
MODULESHOME=/usr/share/Modules
LOADEDMODULES=
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
PERL_LOCAL_LIB_ROOT=:/home/yannick/perl5
PERL_MB_OPT=--install_base /home/yannick/perl5
PERL_MM_OPT=INSTALL_BASE=/home/yannick/perl5
PERL5LIB=/home/yannick/perl5/lib/perl5:
QT_GRAPHICSSYSTEM_CHECKED=1
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
QTLIB=/usr/lib64/qt-3.3/lib
ZSH=/home/yannick/.oh-my-zsh
PYTHONPATH=:/usr/local/lib/python2.7/site-packages:/home/yannick/SOM
PAGER=less
LESS=-R
LSCOLORS=Gxfxcxdxbxegedabagacad
LC_CTYPE=en_US.UTF-8
EDITOR=vim
_=/usr/bin/env

$ R

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.getenv(c("PATH", "LD_LIBRARY_PATH"))
                                                                                                                                                                                                                                                                                                                                                                  PATH
"/usr/local/texlive/2014/bin/x86_64-linux:/usr/lib64/qt-3.3/bin:/home/yannick/perl5/bin:/usr/local/bin/ncbi:/usr/lib64/mpich/bin:/usr/local/bin/kentUtils:/usr/lib64/python2.7/site-packages/gem/gembinaries:/usr/local/bin/fastqc:/usr/lib64/ccache:/usr/local/bin/bowtie2:/usr/local/bin:/usr/bin:/home/yannick/bin:/usr/local/sbin:/usr/sbin:/home/yannick/scripts"
                                                                                                                                                                                                                                                                                                                                                       LD_LIBRARY_PATH
                                                                                                                                                                                                                "/usr/lib64/R/lib:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib"

$ ls /usr/lib64/R/lib /lib /usr/lib
/lib:
alsa                                      libdrm.so.2                         libnss_files.so.2              libxcb-res.so.0
audit                                     libdrm.so.2.4.0                     libnss_hesiod-2.17.so          libxcb-res.so.0.0.0
binfmt.d                                  libEGL.so.1                         libnss_hesiod.so.2             libxcb-screensaver.so.0
bonobo                                    libEGL.so.1.0.0                     libnss_nis-2.17.so             libxcb-screensaver.so.0.0.0
clang                                     libexpat.so.1                       libnss_nisplus-2.17.so         libxcb-shape.so.0
cpp                                       libexpat.so.1.6.0                   libnss_nisplus.so.2            libxcb-shape.so.0.0.0
crda                                      libffi.so.6                         libnss_nis.so.2                libxcb-shm.so.0
cups                                      libffi.so.6.0.1                     libpango-1.0.so.0              libxcb-shm.so.0.0.0
debug                                     libfontconfig.so.1                  libpango-1.0.so.0.3600.8       libxcb.so.1
dkms                                      libfontconfig.so.1.7.0              libpangocairo-1.0.so.0         libxcb.so.1.1.0
dracut                                    libfreebl3.chk                      libpangocairo-1.0.so.0.3600.8  libxcb-sync.so.1
firewalld                                 libfreebl3.so                       libpangoft2-1.0.so.0           libxcb-sync.so.1.0.0
firmware                                  libfreeblpriv3.chk                  libpangoft2-1.0.so.0.3600.8    libxcb-xevie.so.0
games                                     libfreeblpriv3.so                   libpangoxft-1.0.so.0           libxcb-xevie.so.0.0.0
gcc                                       libfreetype.so.6                    libpangoxft-1.0.so.0.3600.8    libxcb-xf86dri.so.0
gconv                                     libfreetype.so.6.10.0               libpciaccess.so.0              libxcb-xf86dri.so.0.0.0
gdk-pixbuf-2.0                            libgailutil.so.18                   libpciaccess.so.0.11.1         libxcb-xfixes.so.0
gems                                      libgailutil.so.18.0.1               libpcprofile.so                libxcb-xfixes.so.0.0.0
gio                                       libgbm.so.1                         libpcre16.so.0                 libxcb-xinerama.so.0
girepository-1.0                          libgbm.so.1.0.0                     libpcre16.so.0.2.0             libxcb-xinerama.so.0.0.0
grub                                      libgcc_s-4.8.5-20150702.so.1        libpcre32.so.0                 libxcb-xinput.so.0
gtk-2.0                                   libgcc_s.so.1                       libpcre32.so.0.0.0             libxcb-xinput.so.0.1.0
i686                                      libgdk_pixbuf-2.0.so.0              libpcrecpp.so.0                libxcb-xkb.so.1
java                                      libgdk_pixbuf-2.0.so.0.3100.6       libpcrecpp.so.0.0.0            libxcb-xkb.so.1.0.0
java-1.5.0                                libgdk_pixbuf_xlib-2.0.so.0         libpcreposix.so.0              libxcb-xselinux.so.0
java-1.6.0                                libgdk_pixbuf_xlib-2.0.so.0.3100.6  libpcreposix.so.0.0.1          libxcb-xselinux.so.0.0.0
java-1.7.0                                libgdk-x11-2.0.so.0                 libpcre.so.1                   libxcb-xtest.so.0
java-1.8.0                                libgdk-x11-2.0.so.0.2400.28         libpcre.so.1.2.0               libxcb-xtest.so.0.0.0
java-ext                                  libgio-2.0.so.0                     libpixman-1.so.0               libxcb-xvmc.so.0
jvm                                       libgio-2.0.so.0.4600.2              libpixman-1.so.0.34.0          libxcb-xvmc.so.0.0.0
jvm-commmon                               libglapi.so.0                       libpng15.so.15                 libxcb-xv.so.0
jvm-exports                               libglapi.so.0.0.0                   libpng15.so.15.13.0            libxcb-xv.so.0.0.0
jvm-private                               libglib-2.0.so.0                    libpthread-2.17.so             libXcomposite.so.1
kbd                                       libglib-2.0.so.0.4600.2             libpthread.so.0                libXcomposite.so.1.0.0
kde3                                      libGL.so.1                          libresolv-2.17.so              libXcursor.so.1
kde4                                      libGL.so.1.2.0                      libresolv.so.2                 libXcursor.so.1.0.2
kdump                                     libgmodule-2.0.so.0                 librt-2.17.so                  libXdamage.so.1
kernel                                    libgmodule-2.0.so.0.4600.2          librt.so.1                     libXdamage.so.1.1.0
krb5                                      libgobject-2.0.so.0                 libSegFault.so                 libXext.so.6
ld-2.17.so                                libgobject-2.0.so.0.4600.2          libselinux.so.1                libXext.so.6.4.0
ld-linux.so.2                             libgraphite2.so.3                   libsepol.so.1                  libXfixes.so.3
libanl-2.17.so                            libgraphite2.so.3.0.1               libSM.so                       libXfixes.so.3.1.0
libanl.so.1                               libgssapi_krb5.so.2                 libSM.so.6                     libXft.so.2
libatk-1.0.so.0                           libgssapi_krb5.so.2.2               libSM.so.6.0.1                 libXft.so.2.3.2
libatk-1.0.so.0.21409.1                   libgssrpc.so.4                      libssl.so.10                   libXinerama.so.1
libaudit.so.1                             libgssrpc.so.4.2                    libssl.so.1.0.1e               libXinerama.so.1.0.0
libaudit.so.1.0.0                         libgthread-2.0.so.0                 libstdc++.so.6                 libXi.so.6
libauparse.so.0                           libgthread-2.0.so.0.4600.2          libstdc++.so.6.0.19            libXi.so.6.1.0
libauparse.so.0.0.0                       libgtk-x11-2.0.so.0                 libthai.so.0                   libXrandr.so.2
libavahi-client.so.3                      libgtk-x11-2.0.so.0.2400.28         libthai.so.0.1.6               libXrandr.so.2.2.0
libavahi-client.so.3.2.9                  libharfbuzz.so.0                    libthread_db-1.0.so            libXrender.so.1
libavahi-common.so.3                      libharfbuzz.so.0.936.0              libthread_db.so.1              libXrender.so.1.3.0
libavahi-common.so.3.5.3                  libICE.so.6                         libtiff.so.5                   libxshmfence.so.1
libBrokenLocale-2.17.so                   libICE.so.6.3.0                     libtiff.so.5.2.0               libxshmfence.so.1.0.0
libBrokenLocale.so.1                      libjasper.so.1                      libtiffxx.so.5                 libXxf86vm.so.1
libc-2.17.so                              libjasper.so.1.0.0                  libtiffxx.so.5.2.0             libXxf86vm.so.1.0.0
libcairo-script-interpreter.so.2          libjbig85.so.2.0                    libutil-2.17.so                libz.so.1
libcairo-script-interpreter.so.2.11400.2  libjbig.so.2.0                      libutil.so.1                   libz.so.1.2.7
libcairo.so.2                             libjpeg.so.62                       libuuid.so.1                   locale
libcairo.so.2.11400.2                     libjpeg.so.62.1.0                   libuuid.so.1.3.0               modprobe.d
libcap-ng.so.0                            libk5crypto.so.3                    libverto.so.1                  modules
libcap-ng.so.0.0.0                        libk5crypto.so.3.1                  libverto.so.1.0.0              modules-load.d
libcidn-2.17.so                           libkdb5.so.8                        libX11.so.6                    mozilla
libcidn.so.1                              libkdb5.so.8.0                      libX11.so.6.3.0                NetworkManager
libcom_err.so.2                           libkeyutils.so.1                    libX11-xcb.so.1                openssl
libcom_err.so.2.1                         libkeyutils.so.1.5                  libX11-xcb.so.1.0.0            pango
libcrypt-2.17.so                          libkms.so.1                         libXau.so.6                    pkgconfig
libcrypto.so.10                           libkms.so.1.0.0                     libXau.so.6.0.0                polkit-1
libcrypto.so.1.0.1e                       libkrad.so.0                        libxcb-composite.so.0          python2.7
libcrypt.so.1                             libkrad.so.0.0                      libxcb-composite.so.0.0.0      rpm
libc.so.6                                 libkrb5.so.3                        libxcb-damage.so.0             rstudio
libcupscgi.so.1                           libkrb5.so.3.3                      libxcb-damage.so.0.0.0         rstudio-server
libcupsimage.so.2                         libkrb5support.so.0                 libxcb-dpms.so.0               rtkaio
libcupsmime.so.1                          libkrb5support.so.0.1               libxcb-dpms.so.0.0.0           sendmail
libcupsppdc.so.1                          liblzma.so.5                        libxcb-dri2.so.0               sendmail.postfix
libcups.so.2                              liblzma.so.5.2.2                    libxcb-dri2.so.0.0.0           slack
libdbus-1.so.3                            libm-2.17.so                        libxcb-dri3.so.0               sse2
libdbus-1.so.3.7.4                        libmemusage.so                      libxcb-dri3.so.0.0.0           sysctl.d
libdl-2.17.so                             libm.so.6                           libxcb-glx.so.0                systemd
libdl.so.2                                libnsl-2.17.so                      libxcb-glx.so.0.0.0            tmpfiles.d
libdrm_amdgpu.so.1                        libnsl.so.1                         libxcb-present.so.0            tuned
libdrm_amdgpu.so.1.0.0                    libnss_compat-2.17.so               libxcb-present.so.0.0.0        udev
libdrm_intel.so.1                         libnss_compat.so.2                  libxcb-randr.so.0              udisks2
libdrm_intel.so.1.0.0                     libnss_db-2.17.so                   libxcb-randr.so.0.1.0          x86_64-redhat-linux6E
libdrm_nouveau.so.2                       libnss_db.so.2                      libxcb-record.so.0             yum-plugins
libdrm_nouveau.so.2.0.0                   libnss_dns-2.17.so                  libxcb-record.so.0.0.0
libdrm_radeon.so.1                        libnss_dns.so.2                     libxcb-render.so.0
libdrm_radeon.so.1.0.1                    libnss_files-2.17.so                libxcb-render.so.0.0.0

/usr/lib:
alsa                                      libdrm.so.2                         libnss_files.so.2              libxcb-res.so.0
audit                                     libdrm.so.2.4.0                     libnss_hesiod-2.17.so          libxcb-res.so.0.0.0
binfmt.d                                  libEGL.so.1                         libnss_hesiod.so.2             libxcb-screensaver.so.0
bonobo                                    libEGL.so.1.0.0                     libnss_nis-2.17.so             libxcb-screensaver.so.0.0.0
clang                                     libexpat.so.1                       libnss_nisplus-2.17.so         libxcb-shape.so.0
cpp                                       libexpat.so.1.6.0                   libnss_nisplus.so.2            libxcb-shape.so.0.0.0
crda                                      libffi.so.6                         libnss_nis.so.2                libxcb-shm.so.0
cups                                      libffi.so.6.0.1                     libpango-1.0.so.0              libxcb-shm.so.0.0.0
debug                                     libfontconfig.so.1                  libpango-1.0.so.0.3600.8       libxcb.so.1
dkms                                      libfontconfig.so.1.7.0              libpangocairo-1.0.so.0         libxcb.so.1.1.0
dracut                                    libfreebl3.chk                      libpangocairo-1.0.so.0.3600.8  libxcb-sync.so.1
firewalld                                 libfreebl3.so                       libpangoft2-1.0.so.0           libxcb-sync.so.1.0.0
firmware                                  libfreeblpriv3.chk                  libpangoft2-1.0.so.0.3600.8    libxcb-xevie.so.0
games                                     libfreeblpriv3.so                   libpangoxft-1.0.so.0           libxcb-xevie.so.0.0.0
gcc                                       libfreetype.so.6                    libpangoxft-1.0.so.0.3600.8    libxcb-xf86dri.so.0
gconv                                     libfreetype.so.6.10.0               libpciaccess.so.0              libxcb-xf86dri.so.0.0.0
gdk-pixbuf-2.0                            libgailutil.so.18                   libpciaccess.so.0.11.1         libxcb-xfixes.so.0
gems                                      libgailutil.so.18.0.1               libpcprofile.so                libxcb-xfixes.so.0.0.0
gio                                       libgbm.so.1                         libpcre16.so.0                 libxcb-xinerama.so.0
girepository-1.0                          libgbm.so.1.0.0                     libpcre16.so.0.2.0             libxcb-xinerama.so.0.0.0
grub                                      libgcc_s-4.8.5-20150702.so.1        libpcre32.so.0                 libxcb-xinput.so.0
gtk-2.0                                   libgcc_s.so.1                       libpcre32.so.0.0.0             libxcb-xinput.so.0.1.0
i686                                      libgdk_pixbuf-2.0.so.0              libpcrecpp.so.0                libxcb-xkb.so.1
java                                      libgdk_pixbuf-2.0.so.0.3100.6       libpcrecpp.so.0.0.0            libxcb-xkb.so.1.0.0
java-1.5.0                                libgdk_pixbuf_xlib-2.0.so.0         libpcreposix.so.0              libxcb-xselinux.so.0
java-1.6.0                                libgdk_pixbuf_xlib-2.0.so.0.3100.6  libpcreposix.so.0.0.1          libxcb-xselinux.so.0.0.0
java-1.7.0                                libgdk-x11-2.0.so.0                 libpcre.so.1                   libxcb-xtest.so.0
java-1.8.0                                libgdk-x11-2.0.so.0.2400.28         libpcre.so.1.2.0               libxcb-xtest.so.0.0.0
java-ext                                  libgio-2.0.so.0                     libpixman-1.so.0               libxcb-xvmc.so.0
jvm                                       libgio-2.0.so.0.4600.2              libpixman-1.so.0.34.0          libxcb-xvmc.so.0.0.0
jvm-commmon                               libglapi.so.0                       libpng15.so.15                 libxcb-xv.so.0
jvm-exports                               libglapi.so.0.0.0                   libpng15.so.15.13.0            libxcb-xv.so.0.0.0
jvm-private                               libglib-2.0.so.0                    libpthread-2.17.so             libXcomposite.so.1
kbd                                       libglib-2.0.so.0.4600.2             libpthread.so.0                libXcomposite.so.1.0.0
kde3                                      libGL.so.1                          libresolv-2.17.so              libXcursor.so.1
kde4                                      libGL.so.1.2.0                      libresolv.so.2                 libXcursor.so.1.0.2
kdump                                     libgmodule-2.0.so.0                 librt-2.17.so                  libXdamage.so.1
kernel                                    libgmodule-2.0.so.0.4600.2          librt.so.1                     libXdamage.so.1.1.0
krb5                                      libgobject-2.0.so.0                 libSegFault.so                 libXext.so.6
ld-2.17.so                                libgobject-2.0.so.0.4600.2          libselinux.so.1                libXext.so.6.4.0
ld-linux.so.2                             libgraphite2.so.3                   libsepol.so.1                  libXfixes.so.3
libanl-2.17.so                            libgraphite2.so.3.0.1               libSM.so                       libXfixes.so.3.1.0
libanl.so.1                               libgssapi_krb5.so.2                 libSM.so.6                     libXft.so.2
libatk-1.0.so.0                           libgssapi_krb5.so.2.2               libSM.so.6.0.1                 libXft.so.2.3.2
libatk-1.0.so.0.21409.1                   libgssrpc.so.4                      libssl.so.10                   libXinerama.so.1
libaudit.so.1                             libgssrpc.so.4.2                    libssl.so.1.0.1e               libXinerama.so.1.0.0
libaudit.so.1.0.0                         libgthread-2.0.so.0                 libstdc++.so.6                 libXi.so.6
libauparse.so.0                           libgthread-2.0.so.0.4600.2          libstdc++.so.6.0.19            libXi.so.6.1.0
libauparse.so.0.0.0                       libgtk-x11-2.0.so.0                 libthai.so.0                   libXrandr.so.2
libavahi-client.so.3                      libgtk-x11-2.0.so.0.2400.28         libthai.so.0.1.6               libXrandr.so.2.2.0
libavahi-client.so.3.2.9                  libharfbuzz.so.0                    libthread_db-1.0.so            libXrender.so.1
libavahi-common.so.3                      libharfbuzz.so.0.936.0              libthread_db.so.1              libXrender.so.1.3.0
libavahi-common.so.3.5.3                  libICE.so.6                         libtiff.so.5                   libxshmfence.so.1
libBrokenLocale-2.17.so                   libICE.so.6.3.0                     libtiff.so.5.2.0               libxshmfence.so.1.0.0
libBrokenLocale.so.1                      libjasper.so.1                      libtiffxx.so.5                 libXxf86vm.so.1
libc-2.17.so                              libjasper.so.1.0.0                  libtiffxx.so.5.2.0             libXxf86vm.so.1.0.0
libcairo-script-interpreter.so.2          libjbig85.so.2.0                    libutil-2.17.so                libz.so.1
libcairo-script-interpreter.so.2.11400.2  libjbig.so.2.0                      libutil.so.1                   libz.so.1.2.7
libcairo.so.2                             libjpeg.so.62                       libuuid.so.1                   locale
libcairo.so.2.11400.2                     libjpeg.so.62.1.0                   libuuid.so.1.3.0               modprobe.d
libcap-ng.so.0                            libk5crypto.so.3                    libverto.so.1                  modules
libcap-ng.so.0.0.0                        libk5crypto.so.3.1                  libverto.so.1.0.0              modules-load.d
libcidn-2.17.so                           libkdb5.so.8                        libX11.so.6                    mozilla
libcidn.so.1                              libkdb5.so.8.0                      libX11.so.6.3.0                NetworkManager
libcom_err.so.2                           libkeyutils.so.1                    libX11-xcb.so.1                openssl
libcom_err.so.2.1                         libkeyutils.so.1.5                  libX11-xcb.so.1.0.0            pango
libcrypt-2.17.so                          libkms.so.1                         libXau.so.6                    pkgconfig
libcrypto.so.10                           libkms.so.1.0.0                     libXau.so.6.0.0                polkit-1
libcrypto.so.1.0.1e                       libkrad.so.0                        libxcb-composite.so.0          python2.7
libcrypt.so.1                             libkrad.so.0.0                      libxcb-composite.so.0.0.0      rpm
libc.so.6                                 libkrb5.so.3                        libxcb-damage.so.0             rstudio
libcupscgi.so.1                           libkrb5.so.3.3                      libxcb-damage.so.0.0.0         rstudio-server
libcupsimage.so.2                         libkrb5support.so.0                 libxcb-dpms.so.0               rtkaio
libcupsmime.so.1                          libkrb5support.so.0.1               libxcb-dpms.so.0.0.0           sendmail
libcupsppdc.so.1                          liblzma.so.5                        libxcb-dri2.so.0               sendmail.postfix
libcups.so.2                              liblzma.so.5.2.2                    libxcb-dri2.so.0.0.0           slack
libdbus-1.so.3                            libm-2.17.so                        libxcb-dri3.so.0               sse2
libdbus-1.so.3.7.4                        libmemusage.so                      libxcb-dri3.so.0.0.0           sysctl.d
libdl-2.17.so                             libm.so.6                           libxcb-glx.so.0                systemd
libdl.so.2                                libnsl-2.17.so                      libxcb-glx.so.0.0.0            tmpfiles.d
libdrm_amdgpu.so.1                        libnsl.so.1                         libxcb-present.so.0            tuned
libdrm_amdgpu.so.1.0.0                    libnss_compat-2.17.so               libxcb-present.so.0.0.0        udev
libdrm_intel.so.1                         libnss_compat.so.2                  libxcb-randr.so.0              udisks2
libdrm_intel.so.1.0.0                     libnss_db-2.17.so                   libxcb-randr.so.0.1.0          x86_64-redhat-linux6E
libdrm_nouveau.so.2                       libnss_db.so.2                      libxcb-record.so.0             yum-plugins
libdrm_nouveau.so.2.0.0                   libnss_dns-2.17.so                  libxcb-record.so.0.0.0
libdrm_radeon.so.1                        libnss_dns.so.2                     libxcb-render.so.0
libdrm_radeon.so.1.0.1                    libnss_files-2.17.so                libxcb-render.so.0.0.0

/usr/lib64/R/lib:
libRblas.so  libRlapack.so  libRrefblas.so  libR.so

$ cat ~/.R/Makevars
CFLAGS=-g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp
CXXFLAGS=-g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp
CXX11FLAGS=-g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp
CXX14FLAGS=-g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp
CXX17FLAGS=-g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp
CXX1XFLAGS=-g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp
MAKE=make -j30

CC=ccache gcc -std=gnu99
CXX=ccache g++
CXX11=ccache g++
CXX14=ccache g++
CXX17=ccache g++
CXX1X=ccache g++

$ cpp -v
Using built-in specs.
COLLECT_GCC=cpp
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC)
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'
 /usr/libexec/gcc/x86_64-redhat-linux/4.8.5/cc1 -E -quiet -v - -mtune=generic -march=x86-64
ignoring nonexistent directory "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../x86_64-redhat-linux/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/lib/gcc/x86_64-redhat-linux/4.8.5/include
 /usr/local/include
 /usr/include
End of search list.

and the end of the compile process for binless

$ MAKE="make -j8" R CMD INSTALL binless
[...]
* installing to library ‘/home/yannick/R/x86_64-redhat-linux-gnu-library/3.5’
* installing *source* package ‘binless’ ...
** libs
ccache g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -UNDEBUG -DUSE_BOOST=1 -I"/home/yannick/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/home/yannick/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/yannick/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I/usr/local/include   -fpic  -g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp -c GFLLibraryTrapezeImpl.cpp -o GFLLibraryTrapezeImpl.o
ccache g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -UNDEBUG -DUSE_BOOST=1 -I"/home/yannick/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/home/yannick/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/yannick/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I/usr/local/include   -fpic  -g -O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs -DNDEBUG -fpic -I/usr/include/R -fopenmp -c csnorm_cpp.cpp -o csnorm_cpp.o
ccache g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o RcppExports.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -L/usr/lib64/R/lib -lR
installing to /home/yannick/R/x86_64-redhat-linux-gnu-library/3.5/binless/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘binless’
    finding HTML links ... done
    CSbdiff-class                           html
    CSbsig-class                            html
    CSdata-class                            html
    CSdiff-class                            html
    CSgroup-class                           html
    CSinter-class                           html
    CSnorm-class                            html
    CSsig-class                             html
    add_bin_bounds_and_distance             html
    bin_all_datasets                        html
    bin_cts_to_mat                          html
    bin_data                                html
    binless                                 html
    categorize_by_new_type                  html
    chromosome_binless                      html
    compress_cts                            html
    create_empty_matrix                     html
    detect_binless_differences              html
    detect_binless_interactions             html
    detect_binned_differences               html
    detect_binned_interactions              html
    di_index                                html
    dset_statistics                         html
    examine_dataset                         html
    fast_binless                            html
    fast_binless_difference                 html
    fresh_start                             html
    fuse_close_cut_sites                    html
    fused_lasso                             html
    gauss_common_muhat_mean                 html
    gauss_common_muhat_mean_biases          html
    gauss_decay                             html
    gauss_decay_muhat_mean                  html
    gauss_decay_optimize                    html
    gauss_dispersion                        html
    gauss_exposures                         html
    gauss_genomic                           html
    gauss_genomic_muhat_mean                html
    gauss_signal                            html
    gauss_signal_muhat_mean                 html
    generate_fake_dataset                   html
    generate_genomic_biases                 html
    get_all_values                          html
    get_binless_differences                 html
    get_binless_interactions                html
    get_binned_differences                  html
    get_binned_interactions                 html
    get_binned_matrices                     html
    get_cs_group_idx                        html
    get_cs_interaction_idx                  html
    get_interactions                        html
    get_ligation_ratio                      html
    get_nzeros                              html
    get_raw_reads                           html
    get_residuals                           html
    get_signal_matrix                       html
    gfl_BIC                                 html
    gfl_compute_initial_state               html
    group_datasets                          html
    has_converged                           html
    initial_guess_decay                     html
    initial_guess_exposures                 html
    initial_guess_genomic                   html
    iterative_normalization                 html
    load_stripped                           html
    merge_cs_norm_datasets                  html
    normalize_binless                       html
    optimize_lambda2                        html
    optimize_lambda2_smooth                 html
    plot_binless_difference_matrix          html
    plot_binless_matrix                     html
    plot_binless_signal_matrix              html
    plot_binned                             html
    plot_diagnostics                        html
    plot_raw                                html
    plot_virtual_4C                         html
    predict_binned_matrices_irls            html
    prepare_difference_estimation           html
    prepare_first_signal_estimation         html
    prepare_for_sparse_cs_norm              html
    prepare_signal_estimation               html
    read_and_prepare                        html
    read_chromosome_binless                 html
    read_tsv                                html
    save_stripped                           html
    subsample_csnorm                        html
    theta.ml                                html
    update_diagnostics                      html
    zoom_csnorm                             html
** building package indices
** testing if installed package can be loaded
* DONE (binless)