chapmanb
commented
5 years ago Thanks for the report, we're discussing this in bcbio/bcbio-nextgen#2886 to try and debug.
Closed jxshi closed 5 years ago
chapmanb
commented
5 years ago Thanks for the report, we're discussing this in bcbio/bcbio-nextgen#2886 to try and debug.
msarahan
commented
5 years ago Thanks @chapmanb - closing as this is a bioconda package, not an anaconda package.
roryk
commented
5 years ago Sorry @msarahan, we might be a little bit confused, there's a bunch of versions of the reportlab package around. This is actually about the reportlab package, though it just came up since it is one of the packages bcbio-nextgen installs.
On a Linux box if you do:
conda create -c pkgs -n reportlab 'python<3.7' reportlab==3.5.23You'll get the broken reportlab package. If you install with -c anaconda or -c conda-forge you won't get a broken one. I'm not actually sure what the pkgs channel is, is that something else not controlled by you all?
msarahan
commented
5 years ago I see. Reopened. The "pkgs" channel is probably your local package cache, which doesn't tell you much. It could come from anywhere.
roryk
commented
5 years ago I think it is coming from here:
https://repo.continuum.io/pkgs/
Here is the full log:
WARNING: A conda environment already exists at '/home/rdk4/local/share/bcbio/anaconda/envs/reportlab'
Remove existing environment (y/[n])? y
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/rdk4/local/share/bcbio/anaconda/envs/reportlab
added / updated specs:
- python[version='<3.7']
- reportlab==3.5.23
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2019.5.15 | 0 126 KB
freetype-2.9.1 | h8a8886c_1 550 KB
libedit-3.1.20181209 | hc058e9b_0 163 KB
libgcc-ng-9.1.0 | hdf63c60_0 5.1 MB
libpng-1.6.37 | hbc83047_0 278 KB
libstdcxx-ng-9.1.0 | hdf63c60_0 3.1 MB
libtiff-4.0.10 | h2733197_2 435 KB
ncurses-6.1 | he6710b0_1 777 KB
olefile-0.46 | py36_0 48 KB
pillow-6.1.0 | py36h34e0f95_0 642 KB
python-3.6.8 | h0371630_0 30.1 MB
readline-7.0 | h7b6447c_5 324 KB
reportlab-3.5.23 | py36he686d34_0 1.4 MB
sqlite-3.29.0 | h7b6447c_0 1.9 MB
tk-8.6.8 | hbc83047_0 2.8 MB
xz-5.2.4 | h14c3975_4 283 KB
zlib-1.2.11 | h7b6447c_3 103 KB
zstd-1.3.7 | h0b5b093_0 401 KB
------------------------------------------------------------
Total: 48.4 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
ca-certificates pkgs/main/linux-64::ca-certificates-2019.5.15-0
freetype pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1
jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
libtiff pkgs/main/linux-64::libtiff-4.0.10-h2733197_2
ncurses pkgs/main/linux-64::ncurses-6.1-he6710b0_1
olefile pkgs/main/linux-64::olefile-0.46-py36_0
openssl pkgs/main/linux-64::openssl-1.1.1c-h7b6447c_1
pillow pkgs/main/linux-64::pillow-6.1.0-py36h34e0f95_0
python pkgs/main/linux-64::python-3.6.8-h0371630_0
readline pkgs/main/linux-64::readline-7.0-h7b6447c_5
reportlab pkgs/main/linux-64::reportlab-3.5.23-py36he686d34_0
sqlite pkgs/main/linux-64::sqlite-3.29.0-h7b6447c_0
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
xz pkgs/main/linux-64::xz-5.2.4-h14c3975_4
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
python-3.6.8 | 30.1 MB | ####################################################################################################################################### | 100%
ncurses-6.1 | 777 KB | ####################################################################################################################################### | 100%
libedit-3.1.20181209 | 163 KB | ####################################################################################################################################### | 100%
ca-certificates-2019 | 126 KB | ####################################################################################################################################### | 100%
xz-5.2.4 | 283 KB | ####################################################################################################################################### | 100%
readline-7.0 | 324 KB | ####################################################################################################################################### | 100%
pillow-6.1.0 | 642 KB | ####################################################################################################################################### | 100%
zstd-1.3.7 | 401 KB | ####################################################################################################################################### | 100%
freetype-2.9.1 | 550 KB | ####################################################################################################################################### | 100%
tk-8.6.8 | 2.8 MB | ####################################################################################################################################### | 100%
sqlite-3.29.0 | 1.9 MB | ####################################################################################################################################### | 100%
libpng-1.6.37 | 278 KB | ####################################################################################################################################### | 100%
olefile-0.46 | 48 KB | ####################################################################################################################################### | 100%
reportlab-3.5.23 | 1.4 MB | | 0% ERROR: Encountered corrupt package tarball at /home/rdk4/local/share/bcbio/anaconda/pkgs/reportlab-3.5.23-py36he686d34_0.conda. Conda has left it in place. Please report this to the maintainers of your package. For the defaults channel, please report to https://github.com/continuumio/anaconda-issues
reportlab-3.5.23 | 1.4 MB | ####################################################################################################################################### | 100%
CondaSystemExit: Exiting 1The mangled file looks like a ZIP file instead of a tarball:
⌂3090% [rdk4@compute-a-16-168:/n … chner/dev/bcbio-nextgen] 127 $ file /home/rdk4/local/share/bcbio/anaconda/pkgs/reportlab-3.5.23-py36he686d34_0.conda
/home/rdk4/local/share/bcbio/anaconda/pkgs/reportlab-3.5.23-py36he686d34_0.conda: Zip archive data, at least v2.0 to extract.conda files are zip files that contain tarballs. https://github.com/conda/conda-package-handling
repo.anaconda.com/pkgs is not a valid channel. only repo.anaconda.com/pkgs/main and other folders under pkgs are.
roryk
commented
5 years ago Gotcha, thanks for clarifying. It looks like it is pulling from pkgs/main from the log:
reportlab pkgs/main/linux-64::reportlab-3.5.23-py36he686d34_0Fixed package is up. Please let us know if you have further issues.
roryk
commented
5 years ago Wow, thanks so much Mike!
Hi,
I was trying to upgrade bcbio-nextgen package using the following command:
The following error message popped up and it stopped install all the other conda packages.
Expected Behavior
It should install all packages without error message.
Steps to Reproduce
Anaconda or Miniconda version:
reportlab-3.5.23
Operating System:
Ubuntu
conda infoconda list --show-channel-urls