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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
BSD 3-Clause "New" or "Revised" License
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not enough free space error when running python build/build_all.py --docker #170

Closed coleslaw481 closed 3 weeks ago

coleslaw481 commented 3 weeks ago

I ran: python build/build_all.py --docker

and on Dockerfile.cptac and subsequent docker files I got the error:

#6 1.585 E: You don't have enough free space in /var/cache/apt/archives/.

See more of the log below:

=> [internal] load build definition from Dockerfile.cptac                 0.0s
 => => transferring dockerfile: 684B                                       0.0s
 => [internal] load .dockerignore                                          0.0s
 => => transferring context: 34B                                           0.0s
 => [internal] load metadata for docker.io/library/python:3.11-slim        1.4s
 => [ 1/10] FROM docker.io/library/python:3.11-slim@sha256:6d2502238109c9  3.6s
 => => resolve docker.io/library/python:3.11-slim@sha256:6d2502238109c929  0.0s
 => => sha256:d844b89b8a09422556582f4ec94e4b9b37a5e429d65 6.92kB / 6.92kB  0.0s
 => => sha256:b0a0cf830b12453b7e15359a804215a7bcccd3788 29.15MB / 29.15MB  0.9s
 => => sha256:72914424168c8ebb0dbb3d0e08eb1d3b5b2a64cc517 3.51MB / 3.51MB  0.5s
 => => sha256:d12a047f1c7ea4f8e51322323d769a331c46fbf44 12.87MB / 12.87MB  0.4s
 => => sha256:6d2502238109c929569ae99355e28890c438cb11bc8 1.65kB / 1.65kB  0.0s
 => => sha256:c1871384ae32a849812b9873f3358328b583bcf69c5 1.37kB / 1.37kB  0.0s
 => => sha256:ab33f1a2f6621fe008081cae7c61b1ac6343eecd65c7de7 244B / 244B  0.5s
 => => sha256:94510a1366bcf144be79366b3176ae5866b43db71c3 3.41MB / 3.41MB  1.0s
 => => extracting sha256:b0a0cf830b12453b7e15359a804215a7bcccd3788e2bcecf  1.3s
 => => extracting sha256:72914424168c8ebb0dbb3d0e08eb1d3b5b2a64cc51745bd6  0.1s
 => => extracting sha256:d12a047f1c7ea4f8e51322323d769a331c46fbf44d958ccc  0.5s
 => => extracting sha256:ab33f1a2f6621fe008081cae7c61b1ac6343eecd65c7de73  0.0s
 => => extracting sha256:94510a1366bcf144be79366b3176ae5866b43db71c3d3818  0.2s
 => [internal] load build context                                          0.0s
 => => transferring context: 14.69kB                                       0.0s
 => [ 2/10] RUN apt-get update --allow-insecure-repositories               2.2s
 => ERROR [ 3/10] RUN apt-get install -y --allow-unauthenticated --fix-mi  1.6s
------
 > [ 3/10] RUN apt-get install -y --allow-unauthenticated --fix-missing gcc-12 build-essential libpq-dev python3-venv:
#6 0.232 Reading package lists...
#6 0.701 Building dependency tree...
#6 0.825 Reading state information...
#6 0.965 The following additional packages will be installed:
#6 0.965   binutils binutils-common binutils-x86-64-linux-gnu bzip2 cpp cpp-12 dirmngr
#6 0.965   dpkg-dev fakeroot fontconfig-config fonts-dejavu-core g++ g++-12 gcc gnupg
#6 0.965   gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf
#6 0.965   gpgsm libabsl20220623 libalgorithm-diff-perl libalgorithm-diff-xs-perl
#6 0.965   libalgorithm-merge-perl libaom3 libasan8 libassuan0 libatomic1 libavif15
#6 0.965   libbinutils libbrotli1 libbsd0 libc-bin libc-dev-bin libc-devtools libc6
#6 0.965   libc6-dev libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libdav1d6 libde265-0
#6 0.965   libdeflate0 libdpkg-perl libfakeroot libfile-fcntllock-perl libfontconfig1
#6 0.965   libfreetype6 libgav1-1 libgcc-12-dev libgd3 libgdbm-compat4 libgomp1
#6 0.966   libgprofng0 libheif1 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo
#6 0.966   libksba8 libldap-2.5-0 libldap-common liblerc4 liblocale-gettext-perl
#6 0.966   liblsan0 libmpc3 libmpfr6 libnpth0 libnsl-dev libnuma1 libperl5.36
#6 0.966   libpng16-16 libpq5 libpython3-stdlib libpython3.11-minimal
#6 0.966   libpython3.11-stdlib libquadmath0 librav1e0 libsasl2-2 libsasl2-modules
#6 0.966   libsasl2-modules-db libssl-dev libstdc++-12-dev libsvtav1enc1 libtiff6
#6 0.967   libtirpc-dev libtsan2 libubsan1 libwebp7 libx11-6 libx11-data libx265-199
#6 0.967   libxau6 libxcb1 libxdmcp6 libxpm4 libyuv0 linux-libc-dev make manpages
#6 0.967   manpages-dev media-types patch perl perl-modules-5.36 pinentry-curses
#6 0.967   python3 python3-distutils python3-lib2to3 python3-minimal python3-pip-whl
#6 0.967   python3-setuptools-whl python3.11 python3.11-minimal python3.11-venv
#6 0.968   rpcsvc-proto xz-utils
#6 0.969 Suggested packages:
#6 0.969   binutils-doc bzip2-doc cpp-doc gcc-12-locales cpp-12-doc dbus-user-session
#6 0.969   libpam-systemd pinentry-gnome3 tor debian-keyring g++-multilib
#6 0.969   g++-12-multilib gcc-12-doc gcc-multilib autoconf automake libtool flex bison
#6 0.969   gdb gcc-doc gcc-12-multilib parcimonie xloadimage scdaemon glibc-doc
#6 0.969   libc-l10n locales libnss-nis libnss-nisplus sensible-utils git bzr
#6 0.969   libgd-tools postgresql-doc-15 libsasl2-modules-gssapi-mit
#6 0.969   | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp
#6 0.969   libsasl2-modules-sql libssl-doc libstdc++-12-doc make-doc man-browser ed
#6 0.969   diffutils-doc perl-doc libterm-readline-gnu-perl
#6 0.969   | libterm-readline-perl-perl libtap-harness-archive-perl pinentry-doc
#6 0.969   python3-doc python3-tk python3.11-doc binfmt-support
#6 1.569 The following NEW packages will be installed:
#6 1.569   binutils binutils-common binutils-x86-64-linux-gnu build-essential bzip2 cpp
#6 1.569   cpp-12 dirmngr dpkg-dev fakeroot fontconfig-config fonts-dejavu-core g++
#6 1.569   g++-12 gcc gcc-12 gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client
#6 1.569   gpg-wks-server gpgconf gpgsm libabsl20220623 libalgorithm-diff-perl
#6 1.569   libalgorithm-diff-xs-perl libalgorithm-merge-perl libaom3 libasan8
#6 1.569   libassuan0 libatomic1 libavif15 libbinutils libbrotli1 libbsd0 libc-dev-bin
#6 1.569   libc-devtools libc6-dev libcc1-0 libcrypt-dev libctf-nobfd0 libctf0
#6 1.569   libdav1d6 libde265-0 libdeflate0 libdpkg-perl libfakeroot
#6 1.569   libfile-fcntllock-perl libfontconfig1 libfreetype6 libgav1-1 libgcc-12-dev
#6 1.570   libgd3 libgdbm-compat4 libgomp1 libgprofng0 libheif1 libisl23 libitm1
#6 1.570   libjansson4 libjbig0 libjpeg62-turbo libksba8 libldap-2.5-0 libldap-common
#6 1.570   liblerc4 liblocale-gettext-perl liblsan0 libmpc3 libmpfr6 libnpth0
#6 1.570   libnsl-dev libnuma1 libperl5.36 libpng16-16 libpq-dev libpq5
#6 1.570   libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0
#6 1.570   librav1e0 libsasl2-2 libsasl2-modules libsasl2-modules-db libssl-dev
#6 1.570   libstdc++-12-dev libsvtav1enc1 libtiff6 libtirpc-dev libtsan2 libubsan1
#6 1.571   libwebp7 libx11-6 libx11-data libx265-199 libxau6 libxcb1 libxdmcp6 libxpm4
#6 1.571   libyuv0 linux-libc-dev make manpages manpages-dev media-types patch perl
#6 1.571   perl-modules-5.36 pinentry-curses python3 python3-distutils python3-lib2to3
#6 1.571   python3-minimal python3-pip-whl python3-setuptools-whl python3-venv
#6 1.571   python3.11 python3.11-minimal python3.11-venv rpcsvc-proto xz-utils
#6 1.572 The following packages will be upgraded:
#6 1.574   libc-bin libc6
#6 1.585 E: You don't have enough free space in /var/cache/apt/archives/.
#6 1.585 2 upgraded, 124 newly installed, 0 to remove and 0 not upgraded.
#6 1.585 Need to get 113 MB of archives.
#6 1.585 After this operation, 429 MB of additional disk space will be used.
------
executor failed running [/bin/sh -c apt-get install -y --allow-unauthenticated --fix-missing gcc-12 build-essential libpq-dev python3-venv]: exit code: 100
broad_sanger
[+] Building 29.3s (5/17)
sgosline commented 3 weeks ago

This has to do with your docker desktop settings on your machine. Pruning your docker images/volumes/containers helps, and also i generally clean out /tmp/ between builds.

I did some googling and found this: https://stackoverflow.com/questions/65291124/docker-you-dont-have-enough-free-space-in-var-cache-apt-archives