Hello,

I tried to install ANCOMBC in RStudio on Ubuntu 20.04 without success. Consequently, I tried installing it on Windows but encountered the same issue. By the way, I am using RStudio version 4.3.3 (Ubuntu), and 4.2.3 (windows)

See below from Ubuntu:

BiocManager::install("ANCOMBC") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org/ Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.3 (2024-02-29) Installing package(s) 'ANCOMBC' also installing the dependencies ‘Cairo’, ‘ggrastr’, ‘scater’, ‘DirichletMultinomial’, ‘Rmpfr’, ‘gsl’, ‘mia’, ‘CVXR’, ‘energy’

x-gzip' length 99417 bytes (97 KB)

downloaded 97 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggrastr_1.0.2.tar.gz' Content type 'application/x-gzip' length 2592994 bytes (2.5 MB)

downloaded 2.5 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/scater_1.28.0.tar.gz' Content type 'application/gzip' length 4089325 bytes (3.9 MB)

downloaded 3.9 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/DirichletMultinomial_1.42.0.tar.gz' Content type 'application/gzip' length 438338 bytes (428 KB)

downloaded 428 KB

trying URL 'https://cloud.r-project.org/src/contrib/Rmpfr_0.9-5.tar.gz' Content type 'application/x-gzip' length 608053 bytes (593 KB)

downloaded 593 KB

trying URL 'https://cloud.r-project.org/src/contrib/gsl_2.1-8.tar.gz' Content type 'application/x-gzip' length 217997 bytes (212 KB)

downloaded 212 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/mia_1.8.0.tar.gz' Content type 'application/gzip' length 2117730 bytes (2.0 MB)

downloaded 2.0 MB

trying URL 'https://cloud.r-project.org/src/contrib/CVXR_1.0-12.tar.gz' Content type 'application/x-gzip' length 844245 bytes (824 KB)

downloaded 824 KB

trying URL 'https://cloud.r-project.org/src/contrib/energy_1.7-11.tar.gz' Content type 'application/x-gzip' length 57897 bytes (56 KB)

downloaded 56 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/ANCOMBC_2.2.2.tar.gz' Content type 'application/gzip' length 1068225 bytes (1.0 MB)

downloaded 1.0 MB

installing source package ‘Cairo’ ... package ‘Cairo’ successfully unpacked and MD5 sums checked using staged installation checking for gcc... gcc 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for sys/wait.h that is POSIX.1 compatible... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... no configure: CAIRO_LIBS is unset, attempting to guess it. configure: CAIRO_CFLAGS= checking if R was compiled with the RConn patch... no checking for cairo.h... no configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package ‘Cairo’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/Cairo’
installing source package ‘DirichletMultinomial’ ... using staged installation libs using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG gsl-config --cflags -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -fdebug-prefix-map=/build/r-base-CIJAF4/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o /bin/bash: gsl-config: command not found gcc -I"/usr/share/R/include" -DNDEBUG gsl-config --cflags -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -fdebug-prefix-map=/build/r-base-CIJAF4/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dirichlet_fit.c -o dirichlet_fit.o /bin/bash: gsl-config: command not found gcc -I"/usr/share/R/include" -DNDEBUG gsl-config --cflags -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -fdebug-prefix-map=/build/r-base-CIJAF4/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dirichlet_fit_main.c -o dirichlet_fit_main.o /bin/bash: gsl-config: command not found dirichlet_fit_main.c:1:10: fatal error: gsl/gsl_rng.h: No such file or directory 1 | #include <gsl/gsl_rng.h> | ^~~~~~~ compilation terminated. make: *** [/usr/lib/R/etc/Makeconf:191: dirichlet_fit_main.o] Error 1 ERROR: compilation failed for package ‘DirichletMultinomial’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/DirichletMultinomial’
installing source package ‘Rmpfr’ ... package ‘Rmpfr’ successfully unpacked and MD5 sums checked using staged installation checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E 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 mpfr.h usability... no checking mpfr.h presence... no checking for mpfr.h... no configure: error: Header file mpfr.h not found; maybe use --with-mpfr-include=INCLUDE_PATH ERROR: configuration failed for package ‘Rmpfr’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/Rmpfr’
installing source package ‘gsl’ ... package ‘gsl’ successfully unpacked and MD5 sums checked using staged installation checking for gcc... gcc 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for gsl-config... no configure: error: gsl-config not found, is GSL installed? ERROR: configuration failed for package ‘gsl’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/gsl’ ERROR: dependency ‘Cairo’ is not available for package ‘ggrastr’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/ggrastr’ ERROR: dependency ‘Rmpfr’ is not available for package ‘CVXR’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/CVXR’ ERROR: dependency ‘gsl’ is not available for package ‘energy’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/energy’ ERROR: dependency ‘ggrastr’ is not available for package ‘scater’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/scater’ ERROR: dependencies ‘scater’, ‘DirichletMultinomial’ are not available for package ‘mia’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/mia’ ERROR: dependencies ‘mia’, ‘CVXR’, ‘energy’ are not available for package ‘ANCOMBC’
removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.3/ANCOMBC’

The downloaded source packages are in ‘/tmp/Rtmp7YRkII/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: codetools, lattice, MASS, nlme, spatial Old packages: 'ape', 'bslib', 'callr', 'data.table', 'datawizard', 'dbplyr', 'dunn.test', 'effectsize', 'ggsci', 'gh', 'htmltools', 'httpuv', 'httr2', 'insight', 'knitr', 'lme4', 'matrixStats', 'munsell', 'performance', 'pkgdown', 'promises', 'quanteda', 'RcppArmadillo', 'reticulate', 'RSQLite', 'rstudioapi', 'sf', 'shiny', 'testthat', 'uwot', 'xfun' Update all/some/none? [a/s/n]: Update all/some/none? [a/s/n]: n Warning messages: 1: In install.packages(...) : installation of package ‘Cairo’ had non-zero exit status 2: In install.packages(...) : installation of package ‘DirichletMultinomial’ had non-zero exit status 3: In install.packages(...) : installation of package ‘Rmpfr’ had non-zero exit status 4: In install.packages(...) : installation of package ‘gsl’ had non-zero exit status 5: In install.packages(...) : installation of package ‘ggrastr’ had non-zero exit status 6: In install.packages(...) : installation of package ‘CVXR’ had non-zero exit status 7: In install.packages(...) : installation of package ‘energy’ had non-zero exit status 8: In install.packages(...) : installation of package ‘scater’ had non-zero exit status 9: In install.packages(...) : installation of package ‘mia’ had non-zero exit status 10: In install.packages(...) : installation of package ‘ANCOMBC’ had non-zero exit status

Help is much appreciated!

FrederickHuangLin / ANCOMBC

Failure to install ANCOMBC neither windows nor Ubuntu #261