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A conda-smithy repository for sage.
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Not functional installation of sage 9.7 #80

Closed Pascal-Ortiz closed 1 year ago

Pascal-Ortiz commented 1 year ago

Comment:

I installed sage 9.7 via conda-forge and my installation of sage does not work, as explained in this post.

My OS is Ubuntu 18.04. First, I installed mamba using the instructions found here.

Then, following the instruction here, I created the sage environment with this command line:

mamba create -n sage sage python=3.9

Then I activated it like this

(base) po@po-ta:~$ conda activate sage

Finally I ran sage:

(sage) po@po-ta:~$ sage

Here is the entire screen output I got:

(sage) po@po-ta:~$ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.7, Release Date: 2022-09-19                     │
│ Using Python 3.9.13. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: sage.all is not available; this is a limited REPL.        ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage:

The sage installation is not functional as the warning explains.

saraedum commented 1 year ago

I cannot reproduce this.

Could you check that you are running the correct version of SageMath, i.e., what's the output of which sage.

Maybe there are some environment variables set that confuse Python here? What's the output of export?

Could you try running sage from a different directory, e.g., cd /tmp/ then sage?

poldolo commented 1 year ago

I have the exact same issue on a stock OpenSuse Tumbleweed.

(sage) paolo@localhost:~> which sage /home/paolo/anaconda3/envs/sage/bin/sage

declare -x ADDR2LINE="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-addr2line" declare -x AR="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-ar" declare -x AS="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-as" declare -x AUDIODRIVER="pulseaudio" declare -x BUILD="x86_64-conda-linux-gnu" declare -x CC="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-cc" declare -x CC_FOR_BUILD="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-cc" declare -x CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include" declare -x CMAKE_ARGS="-DCMAKE_LINKER=/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-strip" declare -x CMAKE_PREFIX_PATH="/home/paolo/anaconda3/envs/sage:/home/paolo/anaconda3/envs/sage/x86_64-conda-linux-gnu/sysroot/usr" declare -x COLORFGBG="15;0" declare -x COLORTERM="truecolor" declare -x CONDA_BACKUP_HOST="localhost.localdomain" declare -x CONDA_BACKUP_JAVA_HOME="/usr/lib64/jvm/jre-openjdk:-" declare -x CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=":-" declare -x CONDA_BUILD_SYSROOT="/home/paolo/anaconda3/envs/sage/x86_64-conda-linux-gnu/sysroot" declare -x CONDA_DEFAULT_ENV="sage" declare -x CONDA_EXE="/home/paolo/anaconda3/bin/conda" declare -x CONDA_PREFIX="/home/paolo/anaconda3/envs/sage" declare -x CONDA_PREFIX_1="/home/paolo/anaconda3" declare -x CONDA_PROMPT_MODIFIER="(sage) " declare -x CONDA_PYTHON_EXE="/home/paolo/anaconda3/bin/python" declare -x CONDA_SHLVL="2" declare -x CONFIG_SITE="/usr/share/site/x86_64-pc-linux-gnu" declare -x CPP="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-cpp" declare -x CPPFLAGS="-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/paolo/anaconda3/envs/sage/include" declare -x CPU="x86_64" declare -x CSHEDIT="emacs" declare -x CXX="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-c++" declare -x CXXFILT="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-c++filt" declare -x CXXFLAGS="-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include" declare -x CXX_FOR_BUILD="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-c++" declare -x DBUS_SESSION_BUS_ADDRESS="unix:path=/run/user/1000/bus" declare -x DEBUGINFOD_URLS="https://debuginfod.opensuse.org/" declare -x DEBUG_CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include" declare -x DEBUG_CPPFLAGS="-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/paolo/anaconda3/envs/sage/include" declare -x DEBUG_CXXFLAGS="-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include" declare -x DEBUG_FFLAGS="-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe" declare -x DEBUG_FORTRANFLAGS="-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe" declare -x DESKTOP_SESSION="/usr/share/xsessions/default" declare -x DISPLAY=":0" declare -x ELFEDIT="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-elfedit" declare -x F77="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gfortran" declare -x F90="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gfortran" declare -x F95="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-f95" declare -x FC="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gfortran" declare -x FFLAGS="-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include" declare -x FORTRANFLAGS="-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/paolo/anaconda3/envs/sage/include" declare -x FROM_HEADER="" declare -x GCC="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gcc" declare -x GCC_AR="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gcc-ar" declare -x GCC_NM="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gcc-nm" declare -x GCC_RANLIB="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gcc-ranlib" declare -x GFORTRAN="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gfortran" declare -x GPG_TTY="/dev/pts/8" declare -x GPROF="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-gprof" declare -x GTK2_RC_FILES="/etc/gtk-2.0/gtkrc:/home/paolo/.gtkrc-2.0:/home/paolo/.config/gtkrc-2.0" declare -x GTK_IM_MODULE="cedilla" declare -x GTK_MODULES="canberra-gtk-module" declare -x GTK_RC_FILES="/etc/gtk/gtkrc:/home/paolo/.gtkrc:/home/paolo/.config/gtkrc" declare -x GXX="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-g++" declare -x G_BROKEN_FILENAMES="1" declare -x G_FILENAME_ENCODING="@locale,UTF-8,ISO-8859-15,CP1252" declare -x HISTSIZE="1000" declare -x HOME="/home/paolo" declare -x HOST="x86_64-conda-linux-gnu" declare -x HOSTNAME="localhost.localdomain" declare -x HOSTTYPE="x86_64" declare -x INVOCATION_ID="470d4601be6f4fd196014a230ed1abd9" declare -x JAVA_BINDIR="/usr/lib64/jvm/jre-openjdk/bin" declare -x JAVA_HOME="/home/paolo/anaconda3/envs/sage" declare -x JAVA_LD_LIBRARY_PATH="/home/paolo/anaconda3/envs/sage/lib/server" declare -x JAVA_ROOT="/usr/lib64/jvm/jre-openjdk" declare -x JOURNAL_STREAM="8:33750" declare -x JRE_HOME="/usr/lib64/jvm/java-11-openjdk-11" declare -x KDE_APPLICATIONS_AS_SCOPE="1" declare -x KDE_FULL_SESSION="true" declare -x KDE_SESSION_UID="1000" declare -x KDE_SESSION_VERSION="5" declare -x KONSOLE_DBUS_SERVICE=":1.48" declare -x KONSOLE_DBUS_SESSION="/Sessions/5" declare -x KONSOLE_DBUS_WINDOW="/Windows/1" declare -x KONSOLE_VERSION="221203" declare -x LANG="en_US.UTF-8" declare -x LANGUAGE="en_US:it:fr" declare -x LC_MEASUREMENT="it_IT.UTF-8" declare -x LC_MONETARY="it_IT.UTF-8" declare -x LC_NUMERIC="it_IT.UTF-8" declare -x LC_TIME="it_IT.UTF-8" declare -x LD="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-ld" declare -x LDFLAGS="-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/paolo/anaconda3/envs/sage/lib -Wl,-rpath-link,/home/paolo/anaconda3/envs/sage/lib -L/home/paolo/anaconda3/envs/sage/lib" declare -x LD_GOLD="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-ld.gold" declare -x LESS="-M -I -R" declare -x LESSCLOSE="lessclose.sh %s %s" declare -x LESSKEY="/usr/etc/lesskey.bin" declare -x LESSOPEN="lessopen.sh %s" declare -x LESS_ADVANCED_PREPROCESSOR="no" declare -x LOGNAME="paolo" declare -x LS_COLORS="no=00:fi=00:di=01;34:ln=00;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=41;33;01:ex=00;32:.cmd=00;32:.exe=01;32:.com=01;32:.bat=01;32:.btm=01;32:.dll=01;32:.tar=00;31:.tgz=00;31:.arc=00;31:.arj=00;31:.taz=00;31:.lha=00;31:.lz4=00;31:.lzh=00;31:.lzma=00;31:.tlz=00;31:.txz=00;31:.tzo=00;31:.t7z=00;31:.zip=00;31:.z=00;31:.Z=00;31:.dz=00;31:.gz=00;31:.lrz=00;31:.lz=00;31:.lzo=00;31:.xz=00;31:.zst=00;31:.tzst=00;31:.bz2=00;31:.bz=00;31:.tbz=00;31:.tbz2=00;31:.tz=00;31:.deb=00;31:.rpm=00;31:.jar=00;31:.war=00;31:.ear=00;31:.sar=00;31:.rar=00;31:.alz=00;31:.ace=00;31:.zoo=00;31:.cpio=00;31:.7z=00;31:.rz=00;31:.cab=00;31:.wim=00;31:.swm=00;31:.dwm=00;31:.esd=00;31:.asf=01;35:.avi=01;35:.bmp=01;35:.cgm=01;35:.dl=01;35:.emf=01;35:.flc=01;35:.fli=01;35:.flv=01;35:.gif=01;35:.gl=01;35:.jpeg=01;35:.jpg=01;35:.m2v=01;35:.m4v=01;35:.mjpeg=01;35:.mjpg=01;35:.mkv=01;35:.mng=01;35:.mov=01;35:.mp4=01;35:.mp4v=01;35:.mpeg=01;35:.mpg=01;35:.nuv=01;35:.ogm=01;35:.pbm=01;35:.pcx=01;35:.pgm=01;35:.png=01;35:.ppm=01;35:.qt=01;35:.rm=01;35:.rmvb=01;35:.svg=01;35:.svgz=01;35:.tga=01;35:.tif=01;35:.tiff=01;35:.vob=01;35:.webm=01;35:.webp=01;35:.wmv=01;35:.xbm=01;35:.xcf=01;35:.xpm=01;35:.xwd=01;35:.yuv=01;35:.ogv=01;35:.ogx=01;35:.aiff=00;32:.ape=00;32:.aac=00;32:.au=00;32:.flac=00;32:.m4a=00;32:.mid=00;32:.midi=00;32:.mka=00;32:.mp3=00;32:.mpc=00;32:.ogg=00;32:.ra=00;32:.voc=00;32:.wav=00;32:.wma=00;32:.wv=00;32:.oga=00;32:.opus=00;32:.spx=00;32:.xspf=00;32:" declare -x LS_OPTIONS="-N --color=tty -T 0" declare -x MACHTYPE="x86_64-suse-linux" declare -x MAIL="/var/mail/paolo" declare -x MANAGERPID="2169" declare -x MANPATH="/usr/local/man:/usr/share/man" declare -x MANPATHISSET="yes" declare -x MATHJAX_DIR="/lib/python3.9/site-packages/notebook/static/components/MathJax" declare -x MINICOM="-c on" declare -x MORE="-sl" declare -x NM="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-nm" declare -x OBJCOPY="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-objcopy" declare -x OBJDUMP="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-objdump" declare -x OLDPWD="/home/paolo" declare -x OSTYPE="linux" declare -x PAGER="less" declare -x PATH="/home/paolo/anaconda3/envs/sage/bin:/home/paolo/anaconda3/condabin:/home/paolo/.local/bin:/home/paolo/bin:/usr/local/bin:/usr/bin:/bin" declare -x PROFILEHOME="" declare -x PROFILEREAD="true" declare -x PWD="/home/paolo" declare -x PYTHONSTARTUP="/etc/pythonstart" declare -x QEMU_AUDIO_DRV="pa" declare -x QT_AUTO_SCREEN_SCALE_FACTOR="0" declare -x QT_IM_MODULE="xim" declare -x QT_IM_SWITCHER="imsw-multi" declare -x RANLIB="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-ranlib" declare -x READELF="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-readelf" declare -x RSTUDIO_WHICH_R="/home/paolo/anaconda3/envs/sage/bin/R" declare -x SAGE_PKGS="/home/paolo/anaconda3/envs/sage/var/lib/sage/installed" declare -x SESSION_MANAGER="local/localhost.localdomain:@/tmp/.ICE-unix/3574,unix/localhost.localdomain:/tmp/.ICE-unix/3574" declare -x SHELL="/bin/bash" declare -x SHELL_SESSION_ID="7d4aeb839ede469d8e4cd179df05672b" declare -x SHLVL="1" declare -x SIZE="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-size" declare -x SSH_ASKPASS="/usr/libexec/ssh/ssh-askpass" declare -x STRINGS="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-strings" declare -x STRIP="/home/paolo/anaconda3/envs/sage/bin/x86_64-conda-linux-gnu-strip" declare -x SYSTEMD_EXEC_PID="3574" declare -x TERM="xterm-256color" declare -x USER="paolo" declare -x VDPAU_DRIVER="va_gl" declare -x VENDOR="suse" declare -x WINDOWID="4194317" declare -x WINDOWMANAGER="/usr/bin/startplasma-x11" declare -x XAUTHLOCALHOSTNAME="localhost.localdomain" declare -x XAUTHORITY="/run/user/1000/xauth_TdfuGV" declare -x XCURSOR_SIZE="24" declare -x XCURSOR_THEME="breeze_cursors" declare -x XDG_CONFIG_DIRS="/home/paolo/.config/kdedefaults:/etc/xdg:/usr/local/etc/xdg:/usr/etc/xdg" declare -x XDG_CURRENT_DESKTOP="KDE" declare -x XDG_DATA_DIRS="/home/paolo/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share" declare -x XDG_RUNTIME_DIR="/run/user/1000" declare -x XDG_SEAT="seat0" declare -x XDG_SEAT_PATH="/org/freedesktop/DisplayManager/Seat0" declare -x XDG_SESSION_CLASS="user" declare -x XDG_SESSION_DESKTOP="KDE" declare -x XDG_SESSION_ID="1" declare -x XDG_SESSION_PATH="/org/freedesktop/DisplayManager/Session0" declare -x XDG_SESSION_TYPE="x11" declare -x XDG_VTNR="7" declare -x XKEYSYMDB="/usr/X11R6/lib/X11/XKeysymDB" declare -x XMODIFIERS="@im=local" declare -x XNLSPATH="/usr/share/X11/nls" declare -x XSESSION_IS_UP="yes" declare -x _CE_CONDA="" declare -x _CE_M="" declare -x _CONDA_PYTHON_SYSCONFIGDATA_NAME="_sysconfigdata_x86_64_conda_cos7_linux_gnu" declare -x build_alias="x86_64-conda-linux-gnu" declare -x host_alias="x86_64-conda-linux-gnu"

From /tmp same Warning.

Paolo.

slel commented 1 year ago

Maybe a locale problem? Might be worth checking whether these help:

export LANG=en_US.UTF-8
export LANGUAGE=en_US.UTF-8
export LC_ALL=en_US.UTF-8
export LC_CTYPE=en_US.UTF-8

Also, conda-forge now has SageMath 9.8.

poldolo commented 1 year ago

Thanks.

I would say we can close the issue as solved: started from scratch with python 3.10 and everything works fine now! SageMath 9.8 indeed.