DESeq2 intstallation error on fedora
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@kperlejewski-16762
Last seen 3.2 years ago

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

deseq2 R fedora qiime • 314 views
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@mikelove
Last seen 5 hours ago
United States

I don’t see the fansi compilation error itself. Can you try to include that? Your sessionInfo may help also

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