Hi,
I am trying to install DESeq2 on my Fedora but I am getting this error.
read.c:548:18: note: each undeclared identifier is reported only once for each function it appears in make: *** [read.o] Error 1 ERROR: compilation failed for package ‘fansi’
* removing ‘/usr/lib64/R/library/fansi’ ERROR: dependency ‘fansi’ is not available for package ‘pillar’
* removing ‘/usr/lib64/R/library/pillar’ ERROR: dependency ‘pillar’ is not available for package ‘tibble’
* removing ‘/usr/lib64/R/library/tibble’ ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
* removing ‘/usr/lib64/R/library/ggplot2’ ERROR: dependency ‘ggplot2’ is not available for package ‘viridis’
* removing ‘/usr/lib64/R/library/viridis’ ERROR: dependencies ‘ggplot2’, ‘viridis’ are not available for package ‘Hmisc’
* removing ‘/usr/lib64/R/library/Hmisc’ ERROR: dependencies ‘RcppArmadillo’, ‘ggplot2’, ‘Hmisc’ are not available for package ‘DESeq2’
* removing ‘/usr/lib64/R/library/DESeq2’
The downloaded source packages are in ‘/tmp/RtmpL2xcJK/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘fansi’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘pillar’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘tibble’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘ggplot2’ had non-zero exit status 5: In install.packages(pkgs
= doing, lib = lib, ...) : installation of package ‘viridis’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘Hmisc’ had non-zero exit status 7: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘DESeq2’ had non-zero exit status
I've read and people suggest to install libcurl4-openssl-dev libxml2-dev and this should fix the problem.
I can't apply this solution because as I understand there are some changes in Ferora's dependencies.
https://fedoraproject.org/wiki/User:Axilleas/GitLab
so when I type:
yum install libxml2-dev
I get:
Loaded plugins: langpacks, refresh-packagekit No package libxml2-dev available.
Error: Nothing to do
but when I type:
yum install libxml2-devel
Loaded plugins: langpacks, refresh-packagekit Package
libxml2-devel-2.9.1-4.fc20.x86_64 already installed and latest version
Nothing to do
The same for libcurl4-openssl-dev / l/ibcurl-devel combination.
Still DESeq is not installed. What should I do? My R version in 3.5. Ferora28
