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/ >