Problem installing Minfi on Cluster
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Goku • 0
@goku
Last seen 5 months ago

Hi 

I was not able to install Minfi on Community Enterprise Operating System (CentOS) on hpc locally. Can someone please help. 

Thanks. Appreciate your help.

Here is the error message. :- 

 

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"

Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

...

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("minfi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘minfi’
also installing the dependencies ‘preprocessCore’, ‘mclust’, ‘quadprog’

...

* installing *source* package ‘preprocessCore’ ...

checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for library containing pthread_create... -lpthread
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: Enabling threading for preprocessCore
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/usc/R/3.4.0/lib64/R/include -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -c R_colSummarize.c -o R_colSummarize.o
...
gcc -std=gnu99 -shared -L/usr/usc/R/3.4.0/lib64/R/lib -L/usr/local/lib64 -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -lpthread -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -lgfortran -lm -lquadmath -L/usr/usc/R/3.4.0/lib64/R/lib -lR
/usr/bin/ld: cannot find -lmkl_gf_lp64
/usr/bin/ld: cannot find -lmkl_gnu_thread
/usr/bin/ld: cannot find -lmkl_core
collect2: error: ld returned 1 exit status
make: *** [preprocessCore.so] Error 1
ERROR: compilation failed for package ‘preprocessCore’
* removing ‘/auto/rcf-proj2/xx/R/x86_64-pc-linux-gnu-library/3.4/preprocessCore’
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/usc/R/3.4.0/lib64/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
gfortran   -fpic  -g -O2  -c mclust.f -o mclust.o
gfortran   -fpic  -g -O2  -c mclustaddson.f -o mclustaddson.o
gcc -std=gnu99 -shared -L/usr/usc/R/3.4.0/lib64/R/lib -L/usr/local/lib64 -o mclust.so init.o mclust.o mclustaddson.o -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/usc/R/3.4.0/lib64/R/lib -lR
/usr/bin/ld: cannot find -lmkl_gf_lp64
/usr/bin/ld: cannot find -lmkl_gnu_thread
/usr/bin/ld: cannot find -lmkl_core
collect2: error: ld returned 1 exit status
make: *** [mclust.so] Error 1
ERROR: compilation failed for package ‘mclust’
* removing ‘/auto/rcf-proj2/xx/R/x86_64-pc-linux-gnu-library/3.4/mclust’
* installing *source* package ‘quadprog’ ...
** package ‘quadprog’ successfully unpacked and MD5 sums checked
** libs
gfortran  -fvisibility=hidden -fpic  -g -O2  -c aind.f -o aind.o
gcc -std=gnu99 -I/usr/usc/R/3.4.0/lib64/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffloat-store   -c -o solve.QP.compact.o solve.QP.compact.f
gfortran -fvisibility=hidden -fpic -g -O2 -ffloat-store   -c -o solve.QP.o solve.QP.f
gfortran  -fvisibility=hidden -fpic  -g -O2  -c util.f -o util.o
gcc -std=gnu99 -shared -L/usr/usc/R/3.4.0/lib64/R/lib -L/usr/local/lib64 -o quadprog.so aind.o init.o solve.QP.compact.o solve.QP.o util.o -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/usc/R/3.4.0/lib64/R/lib -lR
/usr/bin/ld: cannot find -lmkl_gf_lp64
/usr/bin/ld: cannot find -lmkl_gnu_thread
/usr/bin/ld: cannot find -lmkl_core
collect2: error: ld returned 1 exit status
make: *** [quadprog.so] Error 1
ERROR: compilation failed for package ‘quadprog’
* removing ‘/auto/rcf-proj2/xx/R/x86_64-pc-linux-gnu-library/3.4/quadprog’
ERROR: dependencies ‘preprocessCore’, ‘mclust’, ‘quadprog’ are not available for package ‘minfi’
* removing ‘/auto/rcf-proj2/xx/R/x86_64-pc-linux-gnu-library/3.4/minfi’

The downloaded source packages are in
        ‘/tmp/RtmpsP4cD4/downloaded_packages’
installation path not writeable, unable to update packages: boot, car, cluster,
  foreign, lme4, MASS, Matrix, mgcv, network, nlme, quantreg, R2admb, Rcpp,
  RcppEigen, rpart, scatterplot3d, statnet.common, stringi, stringr, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘preprocessCore’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘mclust’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘quadprog’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘minfi’ had non-zero exit status

 

Minfi local installation Centos hpc • 588 views
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@kasper-daniel-hansen-2979
Last seen 10 weeks ago
United States
You have set up your R installation to use MKL, but you have not done it correctly. You need to sort this out with a sysadmin. You could benefit from consulting the R installation manual. This is something you need to fix at the R installation level (I think, unless you have local overrides). Kasper On Wed, Apr 25, 2018 at 10:11 AM, hemantgujar [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User hemantgujar <https: support.bioconductor.org="" u="" 12419=""/> wrote Question: > Problem installing Minfi on Cluster > <https: support.bioconductor.org="" p="" 108272=""/>: > > Hi > > I was not able to install Minfi on Community Enterprise Operating System > (CentOS) on hpc locally. Can someone please help. > > Thanks. Appreciate your help. > > Here is the error message. :- > > > > R version 3.4.0 (2017-04-21) -- "You Stupid Darkness" > > Copyright (C) 2017 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > ... > > > source("https://bioconductor.org/biocLite.R") > Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help > > biocLite("minfi") > BioC_mirror: https://bioconductor.org > Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.0 (2017-04-21). > Installing package(s) ‘minfi’ > also installing the dependencies ‘preprocessCore’, ‘mclust’, ‘quadprog’ > > ... > > * installing *source* package ‘preprocessCore’ ... > > checking for gcc... gcc -std=gnu99 > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for library containing pthread_create... -lpthread > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for stdlib.h... (cached) yes > checking if PTHREAD_STACK_MIN is defined... yes > configure: Enabling threading for preprocessCore > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/usc/R/3.4.0/lib64/R/include -DNDEBUG > -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 > -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 > -fpic -g -O2 -c R_colSummarize.c -o R_colSummarize.o > ... > gcc -std=gnu99 -shared -L/usr/usc/R/3.4.0/lib64/R/lib -L/usr/local/lib64 > -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o > R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o > R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o > log_avg.o log_median.o matrix_functions.o median.o median_log.o > medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o > rma_background4.o rma_common.o weightedkerneldensity.o -lpthread > -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread > -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -lgfortran -lm > -lquadmath -L/usr/usc/R/3.4.0/lib64/R/lib -lR > /usr/bin/ld: cannot find -lmkl_gf_lp64 > /usr/bin/ld: cannot find -lmkl_gnu_thread > /usr/bin/ld: cannot find -lmkl_core > collect2: error: ld returned 1 exit status > make: *** [preprocessCore.so] Error 1 > ERROR: compilation failed for package ‘preprocessCore’ > * removing ‘/auto/rcf-proj2/hg1/R/x86_64-pc-linux-gnu-library/3.4/ > preprocessCore’ > * installing *source* package ‘mclust’ ... > ** package ‘mclust’ successfully unpacked and MD5 sums checked > ** libs > gcc -std=gnu99 -I/usr/usc/R/3.4.0/lib64/R/include -DNDEBUG > -I/usr/local/include -fpic -g -O2 -c init.c -o init.o > gfortran -fpic -g -O2 -c mclust.f -o mclust.o > gfortran -fpic -g -O2 -c mclustaddson.f -o mclustaddson.o > gcc -std=gnu99 -shared -L/usr/usc/R/3.4.0/lib64/R/lib -L/usr/local/lib64 > -o mclust.so init.o mclust.o mclustaddson.o -Wl,--no-as-needed > -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group > -fopenmp -ldl -lpthread -lm -lgfortran -lm -lquadmath -lgfortran -lm > -lquadmath -L/usr/usc/R/3.4.0/lib64/R/lib -lR > /usr/bin/ld: cannot find -lmkl_gf_lp64 > /usr/bin/ld: cannot find -lmkl_gnu_thread > /usr/bin/ld: cannot find -lmkl_core > collect2: error: ld returned 1 exit status > make: *** [mclust.so] Error 1 > ERROR: compilation failed for package ‘mclust’ > * removing ‘/auto/rcf-proj2/hg1/R/x86_64-pc-linux-gnu-library/3.4/mclust’ > * installing *source* package ‘quadprog’ ... > ** package ‘quadprog’ successfully unpacked and MD5 sums checked > ** libs > gfortran -fvisibility=hidden -fpic -g -O2 -c aind.f -o aind.o > gcc -std=gnu99 -I/usr/usc/R/3.4.0/lib64/R/include -DNDEBUG > -I/usr/local/include -fpic -g -O2 -c init.c -o init.o > gfortran -fvisibility=hidden -fpic -g -O2 -ffloat-store -c -o > solve.QP.compact.o solve.QP.compact.f > gfortran -fvisibility=hidden -fpic -g -O2 -ffloat-store -c -o solve.QP.o > solve.QP.f > gfortran -fvisibility=hidden -fpic -g -O2 -c util.f -o util.o > gcc -std=gnu99 -shared -L/usr/usc/R/3.4.0/lib64/R/lib -L/usr/local/lib64 > -o quadprog.so aind.o init.o solve.QP.compact.o solve.QP.o util.o > -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread > -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -lgfortran -lm > -lquadmath -lgfortran -lm -lquadmath -L/usr/usc/R/3.4.0/lib64/R/lib -lR > /usr/bin/ld: cannot find -lmkl_gf_lp64 > /usr/bin/ld: cannot find -lmkl_gnu_thread > /usr/bin/ld: cannot find -lmkl_core > collect2: error: ld returned 1 exit status > make: *** [quadprog.so] Error 1 > ERROR: compilation failed for package ‘quadprog’ > * removing ‘/auto/rcf-proj2/hg1/R/x86_64-pc-linux-gnu-library/3.4/ > quadprog’ > ERROR: dependencies ‘preprocessCore’, ‘mclust’, ‘quadprog’ are not > available for package ‘minfi’ > * removing ‘/auto/rcf-proj2/hg1/R/x86_64-pc-linux-gnu-library/3.4/minfi’ > > The downloaded source packages are in > ‘/tmp/RtmpsP4cD4/downloaded_packages’ > installation path not writeable, unable to update packages: boot, car, > cluster, > foreign, lme4, MASS, Matrix, mgcv, network, nlme, quantreg, R2admb, Rcpp, > RcppEigen, rpart, scatterplot3d, statnet.common, stringi, stringr, > survival > Warning messages: > 1: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘preprocessCore’ had non-zero exit status > 2: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘mclust’ had non-zero exit status > 3: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘quadprog’ had non-zero exit status > 4: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘minfi’ had non-zero exit status > > > > ------------------------------ > > Post tags: Minfi, local installation, Centos, hpc > > You may reply via email or visit https://support.bioconductor. > org/p/108272/ >
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