B - INSTALACAO-NOVOS-PACOTES

560 days ago by jmarcellopereira

INSTALAÇÃO DE NOVOS PACOTES

%sh
sage -i <nome do pacote>

%sh sage -i biopython 
       
WARNING: Output truncated!  
full_output.txt



/tmp/tmpq49Yfo
make build/make/Makefile
make[1]: Entering directory '/home/jmarcellopereira/SageMath'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/jmarcellopereira/SageMath'
build/bin/sage-logger \
	"cd build/make && ./install 'all-toolchain'" logs/install.log
Nothing to (re)build / all up-to-date.

make build/make/Makefile
make[1]: Entering directory '/home/jmarcellopereira/SageMath'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/jmarcellopereira/SageMath'
build/bin/sage-logger \
	"cd build/make && ./install 'biopython'" logs/install.log
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
AR=ar
AS=as
CCACHE_BASEDIR=/home/jmarcellopereira/SageMath
CC=gcc
CHMOD=chmod
COLORFGBG=15;0
COLUMNS=80
CPATH=/home/jmarcellopereira/SageMath/local/include:/usr/include/x86_64-\
linux-gnu
CP=cp
CPP=cpp
CXX=g++
CYSIGNALS_CRASH_DAYS=7
CYSIGNALS_CRASH_LOGS=/home/jmarcellopereira/.sage//crash_logs
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-ezx0xpqJPH,guid=de7b63a\
ed4f89fa8618d7615572ccace
DEFAULTS_PATH=/usr/share/gconf//usr/share/xsessions/plasma.default.path
DESKTOP_SESSION=/usr/share/xsessions/plasma
DISPLAY=:0
DOT_SAGE=/home/jmarcellopereira/.sage/
ECLDIR=/home/jmarcellopereira/SageMath/local/lib/ecl/
F77=gfortran
F90=gfortran
F95=gfortran
FC=gfortran
GIT_EXEC_PATH=/home/jmarcellopereira/SageMath/local/libexec/git-core
GIT_TEMPLATE_DIR=/home/jmarcellopereira/SageMath/local/share/git-core/te\
mplates
GP_DATA_DIR=/home/jmarcellopereira/SageMath/local/share/pari
GPDOCDIR=/home/jmarcellopereira/SageMath/local/share/pari/doc
GPG_AGENT_INFO=/home/jmarcellopereira/.gnupg/S.gpg-agent:0:1
GPHELP=/home/jmarcellopereira/SageMath/local/bin/gphelp
GS_LIB=/home/jmarcellopereira/.fonts
GTK2_RC_FILES=/etc/gtk-2.0/gtkrc:/home/jmarcellopereira/.gtkrc-2.0:/home\
/jmarcellopereira/.config/gtkrc-2.0
GTK_RC_FILES=/etc/gtk/gtkrc:/home/jmarcellopereira/.gtkrc:/home/jmarcell\
opereira/.config/gtkrc
HOME=/home/jmarcellopereira
IPYTHONDIR=/home/jmarcellopereira/.sage//ipython-4.1.2
KDE_FULL_SESSION=true
KDE_MULTIHEAD=false
KDE_SESSION_UID=1000
KDE_SESSION_VERSION=5
KONSOLE_DBUS_SERVICE=:1.80
KONSOLE_DBUS_SESSION=/Sessions/1
KONSOLE_DBUS_WINDOW=/Windows/1
KONSOLE_PROFILE_NAME=Marcello
LANG=en_US.UTF-8

...

SAGE_ETC=/home/jmarcellopereira/SageMath/local/etc
SAGE_EXTCODE=/home/jmarcellopereira/SageMath/local/share/sage/ext
SAGE_LOCAL=/home/jmarcellopereira/SageMath/local
SAGE_LOGS=/home/jmarcellopereira/SageMath/logs/pkgs
SAGE_NUM_THREADS=1
SAGE_NUM_THREADS_PARALLEL=4
SAGE_ORIG_PATH=/home/jmarcellopereira/anaconda2/bin:/home/jmarcelloperei\
ra/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin\
:/bin:/usr/games:/usr/local/games:/snap/bin
SAGE_ORIG_PATH_SET=True
SAGE_REPO_ANONYMOUS=git://trac.sagemath.org/sage.git
SAGE_REPO_AUTHENTICATED=ssh://git@trac.sagemath.org:2222/sage.git
SAGE_ROOT=/home/jmarcellopereira/SageMath
SAGE_SCRIPTS_DIR=/home/jmarcellopereira/SageMath/src/bin
SAGE_SHARE=/home/jmarcellopereira/SageMath/local/share
SAGE_SPKG_INST=/home/jmarcellopereira/SageMath/local/var/lib/sage/instal\
led
SAGE_SPKG=sage-spkg 
SAGE_SRC=/home/jmarcellopereira/SageMath/src
SAGE_STARTUP_FILE=/home/jmarcellopereira/.sage//init.sage
SAGE_VERSION=7.1
SESSION_MANAGER=local/KUBUNTU-16:@/tmp/.ICE-unix/1391,unix/KUBUNTU-16:/t\
mp/.ICE-unix/1391
SHELL=/bin/bash
SHELL_SESSION_ID=7a0fef78a5ce4000a596d1d0396ea676
SHLVL=4
SINGULAR_EXECUTABLE=/home/jmarcellopereira/SageMath/local/bin/Singular
SINGULARPATH=/home/jmarcellopereira/SageMath/local/share/singular
SSH_AGENT_PID=1311
SSH_AUTH_SOCK=/tmp/ssh-TKCsvpD0GBu4/agent.1266
TERMINFO=/home/jmarcellopereira/SageMath/local/share/terminfo
TERM=xterm
TOUCH=touch
UNAME=Linux
USER=jmarcellopereira
_=/usr/bin/env
WINDOWID=106954757
XAUTHORITY=/tmp/xauth-1000-_0
XCURSOR_THEME=breeze_cursors
XDG_CONFIG_DIRS=/etc/xdg/xdg-/usr/share/xsessions/plasma:/etc/xdg:/usr/s\
hare/kubuntu-default-settings/kf5-settings
XDG_CURRENT_DESKTOP=KDE
XDG_DATA_DIRS=/usr/share//usr/share/xsessions/plasma:/usr/local/share/:/\
usr/share/:/var/lib/snapd/desktop
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
XDG_SEAT=seat0
XDG_SESSION_CLASS=user
XDG_SESSION_DESKTOP=KDE
XDG_SESSION_ID=2
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session1
XDG_SESSION_TYPE=x11
XDG_VTNR=7
***********************************************
make[1]: Entering directory '/home/jmarcellopereira/SageMath/build/make'
sage-logger 'sage --pip install biopython'
/home/jmarcellopereira/SageMath/logs/pkgs/biopython.log
Requirement already satisfied (use --upgrade to upgrade): biopython in
/home/jmarcellopereira/SageMath/local/lib/python2.7/site-packages
You are using pip version 8.1.0, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip'
command.
make[1]: Leaving directory '/home/jmarcellopereira/SageMath/build/make'

real	0m1.010s
user	0m0.380s
sys	0m0.080s
Sage build/upgrade complete!
WARNING: Output truncated!  
full_output.txt



/tmp/tmpq49Yfo
make build/make/Makefile
make[1]: Entering directory '/home/jmarcellopereira/SageMath'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/jmarcellopereira/SageMath'
build/bin/sage-logger \
	"cd build/make && ./install 'all-toolchain'" logs/install.log
Nothing to (re)build / all up-to-date.

make build/make/Makefile
make[1]: Entering directory '/home/jmarcellopereira/SageMath'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/jmarcellopereira/SageMath'
build/bin/sage-logger \
	"cd build/make && ./install 'biopython'" logs/install.log
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
AR=ar
AS=as
CCACHE_BASEDIR=/home/jmarcellopereira/SageMath
CC=gcc
CHMOD=chmod
COLORFGBG=15;0
COLUMNS=80
CPATH=/home/jmarcellopereira/SageMath/local/include:/usr/include/x86_64-linux-gnu
CP=cp
CPP=cpp
CXX=g++
CYSIGNALS_CRASH_DAYS=7
CYSIGNALS_CRASH_LOGS=/home/jmarcellopereira/.sage//crash_logs
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-ezx0xpqJPH,guid=de7b63aed4f89fa8618d7615572ccace
DEFAULTS_PATH=/usr/share/gconf//usr/share/xsessions/plasma.default.path
DESKTOP_SESSION=/usr/share/xsessions/plasma
DISPLAY=:0
DOT_SAGE=/home/jmarcellopereira/.sage/
ECLDIR=/home/jmarcellopereira/SageMath/local/lib/ecl/
F77=gfortran
F90=gfortran
F95=gfortran
FC=gfortran
GIT_EXEC_PATH=/home/jmarcellopereira/SageMath/local/libexec/git-core
GIT_TEMPLATE_DIR=/home/jmarcellopereira/SageMath/local/share/git-core/templates
GP_DATA_DIR=/home/jmarcellopereira/SageMath/local/share/pari
GPDOCDIR=/home/jmarcellopereira/SageMath/local/share/pari/doc
GPG_AGENT_INFO=/home/jmarcellopereira/.gnupg/S.gpg-agent:0:1
GPHELP=/home/jmarcellopereira/SageMath/local/bin/gphelp
GS_LIB=/home/jmarcellopereira/.fonts
GTK2_RC_FILES=/etc/gtk-2.0/gtkrc:/home/jmarcellopereira/.gtkrc-2.0:/home/jmarcellopereira/.config/gtkrc-2.0
GTK_RC_FILES=/etc/gtk/gtkrc:/home/jmarcellopereira/.gtkrc:/home/jmarcellopereira/.config/gtkrc
HOME=/home/jmarcellopereira
IPYTHONDIR=/home/jmarcellopereira/.sage//ipython-4.1.2
KDE_FULL_SESSION=true
KDE_MULTIHEAD=false
KDE_SESSION_UID=1000
KDE_SESSION_VERSION=5
KONSOLE_DBUS_SERVICE=:1.80
KONSOLE_DBUS_SESSION=/Sessions/1
KONSOLE_DBUS_WINDOW=/Windows/1
KONSOLE_PROFILE_NAME=Marcello
LANG=en_US.UTF-8

...

SAGE_ETC=/home/jmarcellopereira/SageMath/local/etc
SAGE_EXTCODE=/home/jmarcellopereira/SageMath/local/share/sage/ext
SAGE_LOCAL=/home/jmarcellopereira/SageMath/local
SAGE_LOGS=/home/jmarcellopereira/SageMath/logs/pkgs
SAGE_NUM_THREADS=1
SAGE_NUM_THREADS_PARALLEL=4
SAGE_ORIG_PATH=/home/jmarcellopereira/anaconda2/bin:/home/jmarcellopereira/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
SAGE_ORIG_PATH_SET=True
SAGE_REPO_ANONYMOUS=git://trac.sagemath.org/sage.git
SAGE_REPO_AUTHENTICATED=ssh://git@trac.sagemath.org:2222/sage.git
SAGE_ROOT=/home/jmarcellopereira/SageMath
SAGE_SCRIPTS_DIR=/home/jmarcellopereira/SageMath/src/bin
SAGE_SHARE=/home/jmarcellopereira/SageMath/local/share
SAGE_SPKG_INST=/home/jmarcellopereira/SageMath/local/var/lib/sage/installed
SAGE_SPKG=sage-spkg 
SAGE_SRC=/home/jmarcellopereira/SageMath/src
SAGE_STARTUP_FILE=/home/jmarcellopereira/.sage//init.sage
SAGE_VERSION=7.1
SESSION_MANAGER=local/KUBUNTU-16:@/tmp/.ICE-unix/1391,unix/KUBUNTU-16:/tmp/.ICE-unix/1391
SHELL=/bin/bash
SHELL_SESSION_ID=7a0fef78a5ce4000a596d1d0396ea676
SHLVL=4
SINGULAR_EXECUTABLE=/home/jmarcellopereira/SageMath/local/bin/Singular
SINGULARPATH=/home/jmarcellopereira/SageMath/local/share/singular
SSH_AGENT_PID=1311
SSH_AUTH_SOCK=/tmp/ssh-TKCsvpD0GBu4/agent.1266
TERMINFO=/home/jmarcellopereira/SageMath/local/share/terminfo
TERM=xterm
TOUCH=touch
UNAME=Linux
USER=jmarcellopereira
_=/usr/bin/env
WINDOWID=106954757
XAUTHORITY=/tmp/xauth-1000-_0
XCURSOR_THEME=breeze_cursors
XDG_CONFIG_DIRS=/etc/xdg/xdg-/usr/share/xsessions/plasma:/etc/xdg:/usr/share/kubuntu-default-settings/kf5-settings
XDG_CURRENT_DESKTOP=KDE
XDG_DATA_DIRS=/usr/share//usr/share/xsessions/plasma:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
XDG_SEAT=seat0
XDG_SESSION_CLASS=user
XDG_SESSION_DESKTOP=KDE
XDG_SESSION_ID=2
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session1
XDG_SESSION_TYPE=x11
XDG_VTNR=7
***********************************************
make[1]: Entering directory '/home/jmarcellopereira/SageMath/build/make'
sage-logger 'sage --pip install biopython' /home/jmarcellopereira/SageMath/logs/pkgs/biopython.log
Requirement already satisfied (use --upgrade to upgrade): biopython in /home/jmarcellopereira/SageMath/local/lib/python2.7/site-packages
You are using pip version 8.1.0, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
make[1]: Leaving directory '/home/jmarcellopereira/SageMath/build/make'

real	0m1.010s
user	0m0.380s
sys	0m0.080s
Sage build/upgrade complete!

Usando o Pacote Instalado

import biopython 
       
Traceback (click to the left of this block for traceback)
...
ImportError: No module named biopython
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "_sage_input_5.py", line 10, in <module>
    exec compile(u'open("___code___.py","w").write("# -*- coding: utf-8 -*-\\n" + _support_.preparse_worksheet_cell(base64.b64decode("aW1wb3J0IGJpb3B5dGhvbg=="),globals())+"\\n"); execfile(os.path.abspath("___code___.py"))
  File "", line 1, in <module>
    
  File "/tmp/tmpQvbUnI/___code___.py", line 2, in <module>
    exec compile(u'import biopython
  File "", line 1, in <module>
    
ImportError: No module named biopython