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I'm trying to install package 'DNAcopy' but everytime I install I get this error:

> BiocManager::install('DNAcopy')
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.4 (2021-02-15)
Installing package(s) 'DNAcopy'
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/DNAcopy_1.64.0.tar.gz'
Content type 'application/x-gzip' length 334237 bytes (326 KB)
==================================================
downloaded 326 KB

* installing *source* package ‘DNAcopy’ ...
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c cbsWtstats.f -o cbsWtstats.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c cbststats.f -o cbststats.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c changepoints.f -o changepoints.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c esegment.f -o esegment.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c flchoose.c -o flchoose.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fphyper.c -o fphyper.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fpnorm.c -o fpnorm.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c getbdry.f -o getbdry.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c prune.f -o prune.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rshared.c -o rshared.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c segmentp.f -o segmentp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c smoothCNA.f -o smoothCNA.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong  -c tailprobs.f -o tailprobs.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: DNAcopy.so] Error 1
ERROR: compilation failed for package ‘DNAcopy’
* removing ‘/usr/local/lib/R/site-library/DNAcopy’

The downloaded source packages are in
    ‘/tmp/RtmpiJ39l0/downloaded_packages’
Old packages: 'mgcv'
Update all/some/none? [a/s/n]: a
trying URL 'https://cloud.r-project.org/src/contrib/mgcv_1.8-34.tar.gz'
Content type 'application/x-gzip' length 1149538 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coxph.c -o coxph.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c davies.c -o davies.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c discrete.c -o discrete.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdi.c -o gdi.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c magic.c -o magic.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mat.c -o mat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrix.c -o matrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mgcv.c -o mgcv.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c misc.c -o misc.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mvn.c -o mvn.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c qp.c -o qp.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c soap.c -o soap.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sparse-smooth.c -o sparse-smooth.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sparse.c -o sparse.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tprs.c -o tprs.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: mgcv.so] Error 1
ERROR: compilation failed for package ‘mgcv’
* removing ‘/usr/lib/R/library/mgcv’
* restoring previous ‘/usr/lib/R/library/mgcv’

The downloaded source packages are in
    ‘/tmp/RtmpiJ39l0/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(...) :
  installation of package ‘DNAcopy’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘mgcv’ had non-zero exit status

I have checked and realized that gfortran have been installed

GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 Copyright (C) 2019 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.

I have follow multiple instruction, remove, purge and reinstall gfortran multiple times but its no use. Can anyone help me to solve this problem, please.

Vladimir F Героям слава
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khanhlpbao
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    We provide a catch-all package `r-base-dev` -- try installing that (`sudo apt install r-base-dev`) and it should give you what you need. – Dirk Eddelbuettel Apr 01 '21 at 03:47
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    The other issue may be that you have a different `gcc` version than `gfortran` version. `dpkg -l|grep ...` may tell, as will plain `gcc --version; gfortran --version`. For what it is worth I just installed `DNAcopy` just fine on my Ubuntu 20.10 box. – Dirk Eddelbuettel Apr 01 '21 at 03:51
  • Does this answer your question? [lgfortran not found](https://stackoverflow.com/questions/10881002/lgfortran-not-found) – loonatick Apr 01 '21 at 03:58
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    Which way did you solve it? Using the link suggested by loonatick? Or how? – Vladimir F Героям слава Apr 01 '21 at 09:33
  • I found all neccessary files placed on another folder, so I use sudo cp to copy all of them to /usr/bin/ld – khanhlpbao Apr 02 '21 at 12:16

0 Answers0