Question

Unable to install scde in ubuntu 16.04 , this is what happens when I install scde

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aditya531996 • 0

@aditya531996-12339

Last seen 7.8 years ago

glmFamily.cpp -o glmFamily.o

g++ -I/usr/share/R/include -DNDEBUG -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mcmcsamp.cpp -o mcmcsamp.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimizer.cpp -o optimizer.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c predModule.cpp -o predModule.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c respModule.cpp -o respModule.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lme4.so external.o glmFamily.o mcmcsamp.o optimizer.o predModule.o respModule.o -L/usr/lib/R/lib -lR
installing to /home/aditya/R/x86_64-pc-linux-gnu-library/3.3/lme4/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lme4)
* installing *source* package ‘flexmix’ ...
** package ‘flexmix’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flexmix)
* installing *source* package ‘quantreg’ ...
** package ‘quantreg’ successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -g -O2 -fstack-protector-strong -c akj.f -o akj.o
gfortran -fpic -g -O2 -fstack-protector-strong -c boot.f -o boot.o
gfortran -fpic -g -O2 -fstack-protector-strong -c bound.f -o bound.o
gfortran -fpic -g -O2 -fstack-protector-strong -c boundc.f -o boundc.o
gfortran -fpic -g -O2 -fstack-protector-strong -c brute.f -o brute.o
gfortran -fpic -g -O2 -fstack-protector-strong -c chlfct.f -o chlfct.o
gfortran -fpic -g -O2 -fstack-protector-strong -c cholesky.f -o cholesky.o
gfortran -fpic -g -O2 -fstack-protector-strong -c combos.f -o combos.o
gfortran -fpic -g -O2 -fstack-protector-strong -c crq.f -o crq.o
gfortran -fpic -g -O2 -fstack-protector-strong -c crqfnb.f -o crqfnb.o
gfortran -fpic -g -O2 -fstack-protector-strong -c dsel05.f -o dsel05.o
gfortran -fpic -g -O2 -fstack-protector-strong -c etime.f -o etime.o
gfortran -fpic -g -O2 -fstack-protector-strong -c extract.f -o extract.o
gfortran -fpic -g -O2 -fstack-protector-strong -c idmin.f -o idmin.o
gfortran -fpic -g -O2 -fstack-protector-strong -c iswap.f -o iswap.o
gfortran -fpic -g -O2 -fstack-protector-strong -c kuantile.f -o kuantile.o
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 mcmb.c -o mcmb.o
gfortran -fpic -g -O2 -fstack-protector-strong -c penalty.f -o penalty.o
gfortran -fpic -g -O2 -fstack-protector-strong -c powell.f -o powell.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rls.f -o rls.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rq0.f -o rq0.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rq1.f -o rq1.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rqbr.f -o rqbr.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rqfn.f -o rqfn.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rqfnb.f -o rqfnb.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rqfnc.f -o rqfnc.o
gfortran -fpic -g -O2 -fstack-protector-strong -c rqs.f -o rqs.o
gfortran -fpic -g -O2 -fstack-protector-strong -c sparskit2.f -o sparskit2.o
gfortran -fpic -g -O2 -fstack-protector-strong -c srqfn.f -o srqfn.o
gfortran -fpic -g -O2 -fstack-protector-strong -c srqfnc.f -o srqfnc.o
gfortran -fpic -g -O2 -fstack-protector-strong -c srtpai.f -o srtpai.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o quantreg.so akj.o boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crq.o crqfnb.o dsel05.o etime.o extract.o idmin.o iswap.o kuantile.o mcmb.o penalty.o powell.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o rqs.o sparskit2.o srqfn.o srqfnc.o srtpai.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a(etime.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'quantreg.so' failed
make: *** [quantreg.so] Error 1
ERROR: compilation failed for package ‘quantreg’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/quantreg’
* installing *source* package ‘pbkrtest’ ...
** package ‘pbkrtest’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pbkrtest)
ERROR: dependency ‘quantreg’ is not available for package ‘car’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/car’
ERROR: dependency ‘car’ is not available for package ‘extRemes’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/extRemes’
ERROR: dependencies ‘quantreg’, ‘extRemes’ are not available for package ‘scde’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/scde’

The downloaded source packages are in
‘/tmp/RtmpXFNEIR/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘quantreg’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘car’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘extRemes’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘scde’ had non-zero exit status

scde ubuntu dependencies R • 2.5k views

ADD COMMENT • link updated 7.8 years ago by Martin Morgan 25k • written 7.8 years ago by aditya531996 • 0

Martin Morgan · Answer 1 · 2017-02-13

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

Problems start with installation of the dependency quantreq, so try to get that (e.g., biocLite("quantreg")) to work. From your output

gfortran   -fpic  -g -O2 -fstack-protector-strong  -c etime.f -o etime.o
...
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o quantreg.so akj.o boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crq.o crqfnb.o dsel05.o etime.o extract.o idmin.o iswap.o kuantile.o mcmb.o penalty.o powell.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o rqs.o sparskit2.o srqfn.o srqfnc.o srtpai.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a(etime.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'quantreg.so' failed
make: *** [quantreg.so] Error 1
ERROR: compilation failed for package ‘quantreg’

My guess is that any fortran code fails to compile, e.g,.

/tmp> touch foo.f
/tmp> R CMD SHLIB foo.f

Since R itself installs packages with fortran code I think this means that the version of gfortran your system had at the time of installation (assuming you installed R from source) is different from the version of gfortran you are currently using. So how A: Unable to install DeSeq2 and EdgeR in ubuntu 16.04 , this is what happens when I install R and gfortran (please use the 'COMMENT' button to post comments). On many systems you could use a package manager to install the 'devel' version of R and / or gfortran, e.g.,

sudo apt-get install libgfortran-5-dev

ADD COMMENT • link 7.8 years ago Martin Morgan 25k

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Entering edit mode

When I do sudo apt-get this is what I get 

Reading package lists... Done
Building dependency tree       
Reading state information... Done
libgfortran-5-dev is already the newest version (5.4.1-2ubuntu1~16.04).
0 upgraded, 0 newly installed, 0 to remove and 279 not upgraded.

biocLite("quantreg") gives the following error

gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o quantreg.so akj.o boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crq.o crqfnb.o dsel05.o etime.o extract.o idmin.o iswap.o kuantile.o mcmb.o penalty.o powell.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o rqs.o sparskit2.o srqfn.o srqfnc.o srtpai.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a(etime.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'quantreg.so' failed
make: *** [quantreg.so] Error 1
ERROR: compilation failed for package ‘quantreg’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/quantreg’

The downloaded source packages are in
    ‘/tmp/RtmpHgmmh5/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘quantreg’ had non-zero exit status

Sir , note previously to solve DESeq2 installation I did the following -
http://askubuntu.com/questions/276892/cannot-find-lgfortran

my current gcc using version is

/usr/lib/gcc/x86_64-linux-gnu/4.9/
find /usr/lib/gcc/x86_64-linux-gnu/ -iname "libgfortran"

gives address at

/usr/lib/gcc/x86_64-linux-gnu/5/

So I create a symbolic link

cd /usr/lib/gcc/x86_64-linux-gnu/4.9/
sudo ln -s /usr/lib/gcc/x86_64-linux-gnu/5/libgfortran.a libgfortran.a

ADD REPLY • link updated 7.8 years ago by Martin Morgan 25k • written 7.8 years ago by aditya531996 • 0

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Creating soft links should not be necessary, I would remove it. How did you install R? Again, my temptation would be to remove your installation, and start again using instructions in https://cran.r-project.org/bin/linux/ and using the '-dev' variant to install tools required for installing packages from source.

(It is generally not polite to 'cross-post' http://stackoverflow.com/questions/42196451/quantreg-compilation-causes-libgfortran-a-can-not-be-used-when-making-a-shared because people on the reciprocal sites may each be wasting their time when the other side identifies an appropriate solution. Minimally, reference the cross post. Better, bet on one venue for support and stick with it.)

ADD REPLY • link 7.8 years ago Martin Morgan 25k

score 0 · Answer 2 · 2017-02-13

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theobroma22 ▴ 10

@theobroma22-11920

Last seen 7.9 years ago

Quit R and at the terminal command prompt write R CMD INSTALL scde. This is the same as using install.packages() in R. Did it work?

ADD COMMENT • link 7.8 years ago theobroma22 ▴ 10

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Please always use biocLite(); it is calling install.packages() 'under the hood' but managing repositories so that one does not install packages from incompatible Bioconductor versions.

From the output, it's clear that the problem is not in the installation of scde, but of one of scde's dependencies. So trying to install scde in some round-about way will not solve the problem.

ADD REPLY • link 7.8 years ago Martin Morgan 25k