Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

R libreadline.so.6: R: symbol lookup error: undefined symbol: PC #5350

Closed
mictadlo opened this issue Jul 26, 2017 · 12 comments

Comments

@mictadlo
Copy link
Contributor

@mictadlo mictadlo commented Jul 26, 2017

Hello,
Is it ralated to R or to bioconductor-ballgown=2.2.0=r3.3.2_0 pachterlab/sleuth#128 (comment) ?

Thank you in advance.

Michal

@bgruening

This comment has been minimized.

Copy link
Member

@bgruening bgruening commented Jul 26, 2017

@mictadlo can you please check your channel order. https://bioconda.github.io/#set-up-channels

@mictadlo

This comment has been minimized.

Copy link
Contributor Author

@mictadlo mictadlo commented Jul 27, 2017

Hi do I have to change the order in /home/lorencm/.condarc as describe in your link?

> conda config --show-sources
==> /home/lorencm/.condarc <==
channels:
  - bioconda
  - r
  - defaults
  - conda-forge
@mictadlo

This comment has been minimized.

Copy link
Contributor Author

@mictadlo mictadlo commented Jul 29, 2017

Hi I removed R and reinstalled R with conda insall r

The following NEW packages will be INSTALLED:

    r:             3.3.2-r3.3.2_0   r          
    r-base:        3.3.2-2          conda-forge
    r-boot:        1.3_18-r3.3.2_0  r          
    r-class:       7.3_14-r3.3.2_0  r          
    r-cluster:     2.0.5-r3.3.2_0   r          
    r-codetools:   0.2_15-r3.3.2_0  r          
    r-foreign:     0.8_67-r3.3.2_0  r          
    r-kernsmooth:  2.23_15-r3.3.2_0 r          
    r-lattice:     0.20_34-r3.3.2_0 r          
    r-mass:        7.3_45-r3.3.2_0  r          
    r-matrix:      1.2_7.1-r3.3.2_0 r          
    r-mgcv:        1.8_16-r3.3.2_0  r          
    r-nlme:        3.1_128-r3.3.2_0 r          
    r-nnet:        7.3_12-r3.3.2_0  r          
    r-recommended: 3.3.2-r3.3.2_0   r          
    r-rpart:       4.1_10-r3.3.2_0  r          
    r-spatial:     7.3_11-r3.3.2_0  r          
    r-survival:    2.40_1-r3.3.2_0  r          

Proceed ([y]/n)? 

Why r-base comes from conda-forge but all others one come from r channel?

Thank you in advance.

Michal

@bgruening

This comment has been minimized.

Copy link
Member

@bgruening bgruening commented Jul 29, 2017

You channel order is still wrong. The r channel can be removed and conda-forge before defaults.

@mictadlo

This comment has been minimized.

Copy link
Contributor Author

@mictadlo mictadlo commented Aug 23, 2017

I changed it to:

cat /home/lorencm/.condarc
channels:
  - bioconda
  - conda-forge
  - defaults

but I still got R /work/waterhouse_team/miniconda2/lib/R/bin/exec/R: symbol lookup error: /lustre/work-lustre/waterhouse_team/miniconda2/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

Any ideas?

Thank you in advance

Michal

@romanhaa

This comment has been minimized.

Copy link

@romanhaa romanhaa commented Nov 15, 2017

Just want to chime in and say that I have the same problem after installing r-rmysql. It's kind of a problem since I'm using R every day :/ Let's hope I can fix this quickly.

@bgruening

This comment has been minimized.

Copy link
Member

@bgruening bgruening commented Nov 15, 2017

@romanhaa please make sure the channel order is really correct.
If so you should see something like this:

 conda create -n r r-base -c conda-forge
Fetching package metadata ...............
Solving package specifications: .

Package plan for installation in environment /home/bag/miniconda2/envs/r:

The following NEW packages will be INSTALLED:

    bzip2:           1.0.6-1            conda-forge
    ca-certificates: 2017.7.27.1-0      conda-forge
    cairo:           1.14.6-5           conda-forge
    certifi:         2017.7.27.1-py27_0 conda-forge
    curl:            7.55.1-0           conda-forge
    fontconfig:      2.12.1-5           conda-forge
    freetype:        2.7-2              conda-forge
    gettext:         0.19.7-1           conda-forge
    glib:            2.51.4-0           conda-forge
    graphite2:       1.3.9-0            conda-forge
    gsl:             2.1-2              conda-forge
    harfbuzz:        1.4.3-0            conda-forge
    icu:             58.2-0             conda-forge
    jpeg:            9b-2               conda-forge
    krb5:            1.14.2-0           conda-forge
    libffi:          3.2.1-3            conda-forge
    libgcc:          7.2.0-h69d50b8_2              
    libgcc-ng:       7.2.0-h7cc24e2_2              
    libiconv:        1.14-4             conda-forge
    libpng:          1.6.28-2           conda-forge
    libssh2:         1.8.0-2            conda-forge
    libstdcxx-ng:    7.2.0-h7a57d05_2              
    libtiff:         4.0.7-1            conda-forge
    libxml2:         2.9.5-1            conda-forge
    ncurses:         5.9-10             conda-forge
    openssl:         1.0.2l-0           conda-forge
    pango:           1.40.4-0           conda-forge
    pcre:            8.39-0             conda-forge
    pip:             9.0.1-py27_0       conda-forge
    pixman:          0.34.0-0           conda-forge
    python:          2.7.14-1           conda-forge
    r-base:          3.4.1-2            conda-forge
    readline:        6.2-0              conda-forge
    setuptools:      36.6.0-py27_1      conda-forge
    sqlite:          3.13.0-1           conda-forge
    tk:              8.5.19-2           conda-forge
    wheel:           0.30.0-py_1        conda-forge
    xz:              5.2.3-0            conda-forge
    zlib:            1.2.11-0           conda-forge
@abhi18av

This comment has been minimized.

Copy link

@abhi18av abhi18av commented Dec 23, 2017

I'm facing the same issues. It seems that this bug has been there for a while now.

@bgruening

This comment has been minimized.

Copy link
Member

@bgruening bgruening commented Dec 23, 2017

@abhi18av please also make sure you are using the correct channel order. That means conda-forge has a higher priority than defaults

See also here: https://bioconda.github.io/#set-up-channels

@abhi18av

This comment has been minimized.

Copy link

@abhi18av abhi18av commented Dec 23, 2017

Hi @bgruening . Thanks for the corrections

I fixed it withconda install -c conda-forge readline=6.2

@bgruening

This comment has been minimized.

Copy link
Member

@bgruening bgruening commented Jan 14, 2018

Feel free to reopen if this is still an issue.

@bgruening bgruening closed this Jan 14, 2018
@molgor

This comment has been minimized.

Copy link

@molgor molgor commented Mar 5, 2018

the problem was incompatibility with libreadline.so Great fix thank you!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
5 participants
You can’t perform that action at this time.