trinker/pacman

WGCNA package depends on bioconductor packages, failed.

IgnatiusPang opened this issue · 1 comments

IgnatiusPang commented

Dear trinker,

I'm running R version 3.5.2 (2018-12-20) and had the problem installing the 'WGCNA' CRAN package using the pacman 'p_load' function, as it depends on two Bioconductor packages, 'impute' and preprocessCore. I think Bioconductor recently changed the commands it uses to handle packages installation and updates, which could be the source of the problem. For example:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("impute", version = "3.8")

I've copied below the problems that I had, the way I work around this by installing the two bioconductor packages manually and the sessionInfo()... sorry the session is a bit messy. I've been using the pacman package and it has been great! Thank you!

Kind Regards,

Igy

p_load(WGCNA)
Installing package into ‘/home/ignatius/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
Warning: dependencies ‘impute’, ‘preprocessCore’ are not available
trying URL 'https://cloud.r-project.org/src/contrib/WGCNA_1.66.tar.gz'
Content type 'application/x-gzip' length 1159572 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

ERROR: dependencies ‘impute’, ‘preprocessCore’ are not available for package ‘WGCNA’

  • removing ‘/home/ignatius/R/x86_64-pc-linux-gnu-library/3.5/WGCNA’

The downloaded source packages are in
‘/tmp/Rtmp5X74lg/downloaded_packages’
Warning messages:
1: In utils::install.packages(package, ...) :
installation of package ‘WGCNA’ had non-zero exit status
2: In p_install(package, character.only = TRUE, ...) :
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘WGCNA’
4: In p_load(WGCNA) : Failed to install/load:
WGCNA

p_load(impute)
Installing package into ‘/home/ignatius/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/impute_1.56.0.tar.gz'
Content type 'application/x-gzip' length 641565 bytes (626 KB)
==================================================
downloaded 626 KB

  • installing source package ‘impute’ ...
    ** libs
    gfortran -fpic -g -O2 -fstack-protector-strong -c knnimpute.f -o knnimpute.o
    gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o impute.so knnimpute.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
    installing to /home/ignatius/R/x86_64-pc-linux-gnu-library/3.5/impute/libs
    ** R
    ** data
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (impute)

The downloaded source packages are in
‘/tmp/Rtmp5X74lg/downloaded_packages’

impute installed
Warning message:
package ‘impute’ is not available (for R version 3.5.2)

p_load(preprocessCore)
Installing package into ‘/home/ignatius/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/preprocessCore_1.44.0.tar.gz'
Content type 'application/x-gzip' length 122907 bytes (120 KB)
==================================================
downloaded 120 KB

  • 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... /bin/grep
    checking for egrep... /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/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_colSummarize.c -o R_colSummarize.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_plmd_interfaces.c -o R_plmd_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_plmr_interfaces.c -o R_plmr_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_rlm_interfaces.c -o R_rlm_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_subColSummarize.c -o R_subColSummarize.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c avg.c -o avg.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c avg_log.c -o avg_log.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c biweight.c -o biweight.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init_package.c -o init_package.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log_avg.c -o log_avg.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log_median.c -o log_median.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrix_functions.c -o matrix_functions.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c median.c -o median.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c median_log.c -o median_log.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c medianpolish.c -o medianpolish.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plmd.c -o plmd.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plmr.c -o plmr.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c psi_fns.c -o psi_fns.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnorm.c -o qnorm.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlm.c -o rlm.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlm_anova.c -o rlm_anova.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlm_se.c -o rlm_se.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rma_background4.c -o rma_background4.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rma_common.c -o rma_common.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c weightedkerneldensity.c -o weightedkerneldensity.o
    gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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 -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
    installing to /home/ignatius/R/x86_64-pc-linux-gnu-library/3.5/preprocessCore/libs
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (preprocessCore)

The downloaded source packages are in
‘/tmp/Rtmp5X74lg/downloaded_packages’

preprocessCore installed
Warning message:
package ‘preprocessCore’ is not available (for R version 3.5.2)

if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager")

BiocManager::install("preprocessCore", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'preprocessCore'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/preprocessCore_1.44.0.tar.gz'
Content type 'application/x-gzip' length 122907 bytes (120 KB)
==================================================
downloaded 120 KB

  • 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... /bin/grep
    checking for egrep... /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/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_colSummarize.c -o R_colSummarize.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_plmd_interfaces.c -o R_plmd_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_plmr_interfaces.c -o R_plmr_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_rlm_interfaces.c -o R_rlm_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_subColSummarize.c -o R_subColSummarize.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c avg.c -o avg.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c avg_log.c -o avg_log.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c biweight.c -o biweight.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init_package.c -o init_package.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log_avg.c -o log_avg.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log_median.c -o log_median.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrix_functions.c -o matrix_functions.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c median.c -o median.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c median_log.c -o median_log.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c medianpolish.c -o medianpolish.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plmd.c -o plmd.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plmr.c -o plmr.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c psi_fns.c -o psi_fns.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnorm.c -o qnorm.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlm.c -o rlm.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlm_anova.c -o rlm_anova.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlm_se.c -o rlm_se.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rma_background4.c -o rma_background4.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rma_common.c -o rma_common.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c weightedkerneldensity.c -o weightedkerneldensity.o
    gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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 -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
    installing to /home/ignatius/R/x86_64-pc-linux-gnu-library/3.5/preprocessCore/libs
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (preprocessCore)

The downloaded source packages are in
‘/tmp/Rtmp5X74lg/downloaded_packages’

if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager")

BiocManager::install("impute", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'impute'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/impute_1.56.0.tar.gz'
Content type 'application/x-gzip' length 641565 bytes (626 KB)
==================================================
downloaded 626 KB

  • installing source package ‘impute’ ...
    ** libs
    gfortran -fpic -g -O2 -fstack-protector-strong -c knnimpute.f -o knnimpute.o
    gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o impute.so knnimpute.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
    installing to /home/ignatius/R/x86_64-pc-linux-gnu-library/3.5/impute/libs
    ** R
    ** data
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (impute)

The downloaded source packages are in
‘/tmp/Rtmp5X74lg/downloaded_packages’

p_load(WGCNA)
Installing package into ‘/home/ignatius/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/WGCNA_1.66.tar.gz'
Content type 'application/x-gzip' length 1159572 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

  • installing source package ‘WGCNA’ ...
    ** package ‘WGCNA’ successfully unpacked and MD5 sums checked
    ** libs
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DWITH_THREADS -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c corFunctions-utils.c -o corFunctions-utils.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DWITH_THREADS -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c corFunctions.c -o corFunctions.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DWITH_THREADS -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c myMatrixMultiplication.c -o myMatrixMultiplication.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DWITH_THREADS -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c networkFunctions.c -o networkFunctions.o
    g++ -I"/usr/share/R/include" -DNDEBUG -DWITH_THREADS -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parallelQuantile.cc -o parallelQuantile.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DWITH_THREADS -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pivot.c -o pivot.o
    g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o WGCNA.so corFunctions-utils.o corFunctions.o myMatrixMultiplication.o networkFunctions.o parallelQuantile.o pivot.o -lpthread -L/usr/lib/R/lib -lR
    installing to /home/ignatius/R/x86_64-pc-linux-gnu-library/3.5/WGCNA/libs
    ** R
    ** data
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
    ==========================================================================
  • Package WGCNA 1.66 loaded.
  • Important note: It appears that your system supports multi-threading,
  • but it is not enabled within WGCNA in R.
  • To allow multi-threading within WGCNA with all available cores, use
  •      allowWGCNAThreads()
  • within R. Use disableWGCNAThreads() to disable threading if necessary.
  • Alternatively, set the following environment variable on your system:
  •      ALLOW_WGCNA_THREADS=<number_of_processors>
  • for example
  •      ALLOW_WGCNA_THREADS=8
  • To set the environment variable in linux bash shell, type
  •       export ALLOW_WGCNA_THREADS=8

  • before running R. Other operating systems or shells will

  • have a similar command to achieve the same aim.

==========================================================================

  • DONE (WGCNA)

The downloaded source packages are in
‘/tmp/Rtmp5X74lg/downloaded_packages’

WGCNA installed

  • Package WGCNA 1.66 loaded.
  • Important note: It appears that your system supports multi-threading,
  • but it is not enabled within WGCNA in R.
  • To allow multi-threading within WGCNA with all available cores, use
  •      allowWGCNAThreads()
  • within R. Use disableWGCNAThreads() to disable threading if necessary.
  • Alternatively, set the following environment variable on your system:
  •      ALLOW_WGCNA_THREADS=<number_of_processors>
  • for example
  •      ALLOW_WGCNA_THREADS=8
  • To set the environment variable in linux bash shell, type
  •       export ALLOW_WGCNA_THREADS=8

  • before running R. Other operating systems or shells will

  • have a similar command to achieve the same aim.

==========================================================================

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] WGCNA_1.66 fastcluster_1.1.25 dynamicTreeCut_1.63-1 preprocessCore_1.44.0 impute_1.56.0
[6] pacman_0.5.0 usethis_1.4.0 devtools_2.0.1 reticulate_1.10 energy_1.7-5

loaded via a namespace (and not attached):
[1] matrixStats_0.54.0 fs_1.2.6 fit.models_0.5-14 robust_0.4-18 bit64_0.9-7 doParallel_1.0.14
[7] RColorBrewer_1.1-2 rprojroot_1.3-2 tools_3.5.2 backports_1.1.3 R6_2.3.0 rpart_4.1-13
[13] Hmisc_4.1-1 DBI_1.0.0 lazyeval_0.2.1 BiocGenerics_0.28.0 colorspace_1.4-0 nnet_7.3-12
[19] withr_2.1.2 tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2 processx_3.2.1 bit_1.1-14
[25] curl_3.3 compiler_3.5.2 cli_1.0.1 Biobase_2.42.0 htmlTable_1.13.1 desc_1.2.0
[31] scales_1.0.0 checkmate_1.9.1 mvtnorm_1.0-8 DEoptimR_1.0-8 robustbase_0.93-3 callr_3.1.1
[37] stringr_1.3.1 digest_0.6.18 foreign_0.8-71 rrcov_1.4-7 base64enc_0.1-3 pkgconfig_2.0.2
[43] htmltools_0.3.6 sessioninfo_1.1.1 htmlwidgets_1.3 rlang_0.3.1 rstudioapi_0.9.0 RSQLite_2.1.1
[49] bindr_0.1.1 jsonlite_1.6 acepack_1.4.1 dplyr_0.7.8 magrittr_1.5 GO.db_3.7.0
[55] Formula_1.2-3 Matrix_1.2-15 Rcpp_1.0.0 munsell_0.5.0 S4Vectors_0.20.1 stringi_1.2.4
[61] yaml_2.2.0 MASS_7.3-51.1 pkgbuild_1.0.2 plyr_1.8.4 grid_3.5.2 blob_1.1.1
[67] parallel_3.5.2 crayon_1.3.4 lattice_0.20-38 splines_3.5.2 knitr_1.21 ps_1.3.0
[73] pillar_1.3.1 boot_1.3-20 codetools_0.2-16 stats4_3.5.2 pkgload_1.0.2 glue_1.3.0
[79] latticeExtra_0.6-28 data.table_1.12.0 remotes_2.0.2 BiocManager_1.30.4 foreach_1.4.4 testthat_2.0.1
[85] gtable_0.2.0 purrr_0.2.5 assertthat_0.2.0 ggplot2_3.1.0 xfun_0.4 pcaPP_1.9-73
[91] survival_2.43-3 tibble_2.0.1 iterators_1.0.10 AnnotationDbi_1.44.0 memoise_1.1.0 IRanges_2.16.0
[97] bindrcpp_0.2.2 cluster_2.0.7-1

mingjie-bio commented

install.packages("BiocManager")
BiocManager::install("WGCNA")

https://www.bioconductor.org/install/#install-bioconductor-packages