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mooc-rr-ressources
Commit fa518547 authored by Arnaud Legrand's avatar Arnaud Legrand
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Improve the text on pip + information on R installed packages

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module4/ressources/resources.org
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...@@ -83,7 +83,11 @@ hash) will not be stored in the cell. This is not really a problem and ...@@ -83,7 +83,11 @@ hash) will not be stored in the cell. This is not really a problem and
is the price to pay for running git from within the notebook itself. is the price to pay for running git from within the notebook itself.
* Getting information about Python(3) libraries * Getting information about Python(3) libraries
** Getting the list of installed packages and their version ** Getting the list of installed packages and their version
https://stackoverflow.com/questions/20180543/how-to-check-version-of-python-modules This topic is discussed on [[https://stackoverflow.com/questions/20180543/how-to-check-version-of-python-modules][StackOverflow]]. When using =pip= (the Python
package installer) within a shell command, it is easy to query the
version of all installed packages (note that on your system, you may
have to use either =pip= or =pip3= depending on how it is named and which
versions of Python are available on your machine.
#+begin_src shell :results output :exports both #+begin_src shell :results output :exports both
pip3 freeze pip3 freeze
#+end_src #+end_src
...@@ -109,6 +113,10 @@ wcwidth==0.1.7 ...@@ -109,6 +113,10 @@ wcwidth==0.1.7
webencodings==0.5 webencodings==0.5
#+end_example #+end_example
Once you know which packages are installed, you can easily get
additional information about a given package and in particular check
whether it was installed "locally" through pip or whether it is
installed system-wide. Again, in a shell command:
#+begin_src shell :results output :exports both #+begin_src shell :results output :exports both
pip3 show pandas pip3 show pandas
echo " " echo " "
...@@ -138,14 +146,12 @@ Location: /home/alegrand/.local/lib/python3.6/site-packages ...@@ -138,14 +146,12 @@ Location: /home/alegrand/.local/lib/python3.6/site-packages
Requires: patsy, pandas Requires: patsy, pandas
#+end_example #+end_example
#+begin_src python :results output :exports both
#+end_src
** How to list imported modules? ** How to list imported modules?
Inspiring from [[https://stackoverflow.com/questions/4858100/how-to-list-imported-modules][StackOverflow]], here is a simple function that lists Without resorting to pip (that will list all available packages), you
loaded package (that have a =__version__= attribute, which is may want to know which modules are loaded in a Python session as well
unfortunately not completely standard). as their version. Inspiring from [[https://stackoverflow.com/questions/4858100/how-to-list-imported-modules][StackOverflow]], here is a simple
function that lists loaded package (that have a =__version__= attribute,
which is unfortunately not completely standard).
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
def print_imported_modules(): def print_imported_modules():
...@@ -204,9 +210,9 @@ pip3 freeze > requirements.txt # to obtain the list of packages with their versi ...@@ -204,9 +210,9 @@ pip3 freeze > requirements.txt # to obtain the list of packages with their versi
pip3 install -r requirements.txt # to install the previous list of packages, possibly on an other machine pip3 install -r requirements.txt # to install the previous list of packages, possibly on an other machine
#+end_src #+end_src
If you want to have several installed python environments, you may If you want to have several installed Python environments, you may
want to use [[https://docs.pipenv.org/][Pipenv]]. I doubt it allows to track correctly FORTRAN or C want to use [[https://docs.pipenv.org/][Pipenv]]. I doubt it allows to track correctly FORTRAN or C
dynamic libraries that are wrapped by Python. dynamic libraries that are wrapped by Python though.
* Getting information about R libraries * Getting information about R libraries
The best way seems to be to rely on the =devtools= package. The best way seems to be to rely on the =devtools= package.
...@@ -267,3 +273,23 @@ Packages ---------------------------------------------------------------------- ...@@ -267,3 +273,23 @@ Packages ----------------------------------------------------------------------
Some actually advocate that [[https://github.com/ropensci/rrrpkg][writing a reproducible research compendium Some actually advocate that [[https://github.com/ropensci/rrrpkg][writing a reproducible research compendium
can be done by writing an R package]]. Those of you willing to have a can be done by writing an R package]]. Those of you willing to have a
clean R dependency management should thus have a look at [[https://rstudio.github.io/packrat/][Packrat]]. clean R dependency management should thus have a look at [[https://rstudio.github.io/packrat/][Packrat]].
Finally, it is good to know that there is a built-in R command
(=installed.packages=) allowing to retrieve and list the details of all
packages installed.
#+begin_src R :results table :session *R* :exports both :colnames yes
head(installed.packages())
#+end_src
#+RESULTS:
| Package | LibPath | Version | Priority | Depends | Imports | LinkingTo | Suggests | Enhances | License | License_is_FOSS | License_restricts_use | OS_type | MD5sum | NeedsCompilation | Built | |
|-------------------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+-------------+----------------------------------------------------------+----------------------------------------------------------------+-----------+---------------+---------------------------------------+---------------------------+---------------+---------------------+--------+--------+------------------+-------+-------|
| BH | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 | 1.66.0-1 | nil | nil | nil | nil | nil | nil | BSL-1.0 | nil | nil | nil | nil | no | 3.5.1 | |
| Formula | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 | 1.2-3 | nil | R (>= 2.0.0), stats | nil | nil | nil | nil | GPL-2 | GPL-3 | nil | nil | nil | nil | no | 3.5.1 |
| Hmisc | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 | 4.1-1 | nil | lattice, survival (>= 2.40-1), Formula, ggplot2 (>= 2.2) | methods, latticeExtra, cluster, rpart, nnet, acepack, foreign, | | | | | | | | | | | |
| gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), | | | | | | | | | | | | | | | | |
| viridis, htmltools, base64enc | nil | chron, rms, mice, tables, knitr, ff, ffbase, plotly (>= | | | | | | | | | | | | | | |
| 4.5.6) | nil | GPL (>= 2) | nil | nil | nil | nil | yes | 3.5.1 | | | | | | | | |
| Matrix | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 | 1.2-14 | recommended | R (>= 3.2.0) | methods, graphics, grid, stats, utils, lattice | nil | expm, MASS | MatrixModels, graph, SparseM, sfsmisc | GPL (>= 2) | file LICENCE | nil | nil | nil | nil | yes | 3.5.1 |
| StanHeaders | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 | 2.17.2 | nil | nil | nil | nil | RcppEigen, BH | nil | BSD_3_clause + file LICENSE | nil | nil | nil | nil | yes | 3.5.1 | |
| acepack | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 | 1.4.1 | nil | nil | nil | nil | testthat | nil | MIT + file LICENSE | nil | nil | nil | nil | yes | 3.5.1 | |
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