rebuild packages that have a short prefix-lengths

[Michael Remmert]

I have the problem that I have to install conda in a path that is longer than 80 characters, but I still have packages with binary prefixes shorter than 255 characters:

./bin/conda inspect prefix-lengths pkgs/*.bz2
Packages with binary prefixes shorter than 255 characters:
pkgs/ncurses-5.9-8.tar.bz2 (80 chars)
pkgs/r-base-3.2.2-0.tar.bz2 (80 chars)
pkgs/glib-2.43.0-2.tar.bz2 (80 chars)
pkgs/samtools-1.3.1-4.tar.bz2 (80 chars)
pkgs/harfbuzz-0.9.35-6.tar.bz2 (80 chars)
pkgs/pysam-0.9.1.4-py27_0.tar.bz2 (80 chars)
pkgs/pango-1.36.8-3.tar.bz2 (80 chars)

Is there any chance to rebuild these package with long prefixes by myself? Or is there anything else I can do to get these packages working in a path with more than 80 characters?

Thanks for helping!

[Ray Donnelly]

Only packages to which binary prefix replacement needs to be performed
need to be rebuilt to the new prefix length so you are probably ok.

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[Michael Remmert]

Thanks for the tip, but only 2 of these packages could be installed (samtools and pysam), for the others I get these error messages:

PaddingError: Placeholder of length '80' too short in package pkgs::ncurses-5.9-8.
The package must be rebuilt with conda-build > 2.0.
PaddingError: Placeholder of length '80' too short in package pkgs::r-base-3.2.2-0.
The package must be rebuilt with conda-build > 2.0.
PaddingError: Placeholder of length '80' too short in package pkgs::glib-2.43.0-2.
The package must be rebuilt with conda-build > 2.0.
PaddingError: Placeholder of length '80' too short in package pkgs::harfbuzz-0.9.35-6.
The package must be rebuilt with conda-build > 2.0.
PaddingError: Placeholder of length '80' too short in package pkgs::pango-1.36.8-3.
The package must be rebuilt with conda-build > 2.0.

[Ray Donnelly]

Thing is, these are old package versions anyway. The current r-base is
version 3.3.1. Please update them to the latest and try again.

On Wed, Nov 16, 2016 at 5:08 PM, 'Michael Remmert' via conda - Public

> https://groups.google.com/a/continuum.io/d/msgid/conda/486c6279-dcf3-4154-bd66-a1efb05fbb39%40continuum.io.

[Michael Sarahan]

This may be a caching problem.  Conda won't download new versions if it's happy with the ones that it already has.

You might need to clean up your cache:

conda clean -pt

To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/conda/CAF5kcVVizLLs4B3AbVoG%3DzHu4pAhToiUMjKJqvJnts1Td_yn_w%40mail.gmail.com.

[Michael Remmert]

I can't update to the newest version, because conda itself downgraded the R version while installing some R packages.

[Ray Donnelly]

Which ones? I need to fix that.

On Wed, Nov 16, 2016 at 5:18 PM, 'Michael Remmert' via conda - Public

> https://groups.google.com/a/continuum.io/d/msgid/conda/435fc388-80c1-4168-87c7-0db2ab2a5edd%40continuum.io.

[Michael Remmert]

For the following commands, conda will downgrade the R package:

./conda install -c R -c bioconda bioconductor-diffbind
./conda install -c R -c bioconda bioconductor-bubbletree

The following packages will be DOWNGRADED due to dependency conflicts:

    r:                                 3.3.1-r3.3.1_0        R        --> 3.2.2-0           R
    r-base:                            3.3.1-5               R        --> 3.2.2-0           R
    r-boot:                            1.3_18-r3.3.1_0       R        --> 1.3_17-r3.2.2_0a  R
    r-cluster:                         2.0.4-r3.3.1_0        R        --> 2.0.3-r3.2.2_0a   R
    r-matrix:                          1.2_6-r3.3.1_0        R        --> 1.2_2-r3.2.2_0a   R
    r-mgcv:                            1.8_12-r3.3.1_0       R        --> 1.8_9-r3.2.2_0a   R
    r-nlme:                            3.1_128-r3.3.1_0      R        --> 3.1_122-r3.2.2_0a R
    r-nnet:                            7.3_12-r3.3.1_0       R        --> 7.3_11-r3.2.2_0a  R
    r-recommended:                     3.3.1-r3.3.1_0        R        --> 3.2.2-r3.2.2_0    R
    r-survival:                        2.39_4-r3.3.1_0       R        --> 2.38_3-r3.2.2_0a  R



[Ray Donnelly]

Ah sorry, this is a bioconda issue. They have packages that depend on
the old R version. You need them to update these.

On Wed, Nov 16, 2016 at 5:34 PM, 'Michael Remmert' via conda - Public

> https://groups.google.com/a/continuum.io/d/msgid/conda/0ec129ab-2c9c-44c6-8259-35872b72dfa3%40continuum.io.