Question: DESeq2 intstallation error on fedora
0
gravatar for kperlejewski
16 months ago by
kperlejewski0 wrote:

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 • 176 views
ADD COMMENTlink modified 16 months ago by Michael Love26k • written 16 months ago by kperlejewski0
Answer: DESeq2 intstallation error on fedora
0
gravatar for Michael Love
16 months ago by
Michael Love26k
United States
Michael Love26k wrote:

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

ADD COMMENTlink written 16 months ago by Michael Love26k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 168 users visited in the last hour