I'm trying to install Grothendieck_Schemes from
https://www.isa-afp.org/entries/Grothendieck_Schemes.html#
I downloaded the tar and uncompressed it. The contents are
$ ls -l
Comm_Ring.thy
Group_Extras.thy
ROOT
Scheme.thy
Set_Extras.thy
Topological_Space.thy
document/
root.bib
root.tex
Then I run
$ isabelle components -u ./Downloads/Grothendieck_Schemes/
Added component "/home/username/Downloads/Grothendieck_Schemes"
but when I start Isabelle I get error
C:\Users\Aleksander\.isabelle\Isabelle2022\jedit\jars\isabelle_jedit_main.jar:
Cannot start:
*** Bad imports session "Jacobson_Basic_Algebra" for "Grothendieck_Schemes" (line 3 of "/home/username/Downloads/Grothendieck_Schemes/ROOT")
So I suppose I should install the dependency "Jacobson_Basic_Algebra"? But there is no such package on AFP. I'm thinking that maybe I should have removed the ROOT file. It's contents are
chapter AFP
session "Grothendieck_Schemes" (AFP) = HOL +
options [timeout = 600]
sessions
"Jacobson_Basic_Algebra"
theories
Scheme
document_files
"root.tex"
"root.bib"
I tried running this instead but it fails
$ isabelle components -u ./Downloads/Grothendieck_Schemes/*.thy
*** Bad component directory: "/home/username/Downloads/Grothendieck_Schemes/Comm_Ring.thy"
How do I install these packages properly?
Related
Here's what I'm doing:
I have a blog that uses blogdown to render .Rmd files.
Some of the code snippets in the blog are in Python. I'm using reticulate for that.
I'm using a GitHub workflow to build and publish the blog as part of a larger website. This workflow sets up the environment and package dependencies in miniconda.
The last time this ran was six months ago. At that time, it worked. Now, it does not. I can't seem to replicate the behavior locally for more detailed debugging.
It seems to be trying to put a mamba command into normalizePath instead of a filesystem path (www-main is the name of the repository):
conda activate www-main
Rscript -e 'blogdown::build_site(local=FALSE, run_hugo=FALSE, build_rmd="content/blog/2020-08-28-api.Rmd")'
shell: /usr/bin/bash -l {0}
env:
CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir
Rendering content/blog/2020-08-28-api.Rmd...
[...]
Quitting from lines 401-410 (2020-08-28-api.Rmd)
Error in normalizePath(conda, winslash = "/", mustWork = TRUE) :
path[1]="# cmd: /usr/share/miniconda/condabin/mamba update --name www-main --file /home/runner/work/www-main/www-main/conda": No such file or directory
Calls: local ... python_munge_path -> get_python_conda_info -> normalizePath
Execution halted
Error: Failed to render content/blog/2020-08-28-api.Rmd
Execution halted
Lines 401-410 of 2020-08-28-api.Rmd are a Python code block:
400 ```{python python-data, dev='svg'}
401 import covidcast
402 from datetime import date
403 import matplotlib.pyplot as plt
404
405 data = covidcast.signal("fb-survey", "smoothed_hh_cmnty_cli",
406 date(2020, 9, 8), date(2020, 9, 8),
407 geo_type="state")
408 covidcast.plot_choropleth(data, figsize=(7, 5))
409 plt.title("% who know someone who is sick, Sept 8, 2020")
410 ```
The useful bits of the output of conda info, in case it helps:
active environment : www-main
active env location : /usr/share/miniconda/envs/www-main
shell level : 1
user config file : /home/runner/.condarc
populated config files : /home/runner/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.15.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /usr/share/miniconda (writable)
conda av data dir : /usr/share/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/runner/conda_pkgs_dir
envs directories : /usr/share/miniconda/envs
/home/runner/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-1020-azure ubuntu/20.04.5 glibc/2.31
UID:GID : 1001:121
netrc file : None
offline mode : False
I found this, but their workaround doesn't make sense for me since I'm not using papermill: https://github.com/rstudio/reticulate/issues/1184
I found this, but my paths don't have spaces: https://github.com/rstudio/reticulate/issues/1149
I found this, but their problem includes an entirely reasonable value for path[1], unlike mine: How can I tell R where the conda environment is via a docker image?
The build environment for this is a bit of a bear but I can probably put together a minimum working (/nonworking) example if needed, lmk
I tracked this down to at least two bits of weird/buggy behavior in reticulate and found a workaround: switch from vanilla miniconda to Mambaforge.
The TL;DR seems to be that whatever wacky ubuntu-latest setup-miniconda#v2 environment started putting into meta/history doesn't include a create line, which is what reticulate needs in order to figure out which conda goes with which python, because (1) it ignores the reticulate.conda_binary setting for some reason, and (2) it uses a more restrictive regex to parse the lines of the history file than the regex it uses to select them. Mambaforge does include the create line, so reticulate is happy.
- uses: conda-incubator/setup-miniconda#v2
with:
python-version: 3.9
activate-environment: www-main
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
use-only-tar-bz2: true # (for caching support)
- name: Update environment
run: mamba env update -n www-main -f environment.yml
I was running make and encountered the following error:
gawk: error while loading shared libraries: libreadline.so.4: cannot open shared object file: No such file or directory
config.status: error: could not create mjson.pc
Reaping losing child 0x564b30cbed70 PID 48255
make[1]: *** [Makefile:44: libmjson] Error 1
Removing child 0x564b30cbed70 PID 48255 from chain.
make[1]: Leaving directory '/home/minipc/econet/apps/public/libjson-1.5'
The libreadline.so.4 is too old to install in my current Linux machine (Ubuntu 20.04). So instead I installed libreadline.so.8, and created a symbolic link to libreadline.so.4. And I checked, it works:
lrwxrwxrwx 1 root root 25 Aug 12 21:17 /lib32/libreadline.so.4 -> /lib32/libreadline.so.8.0
lrwxrwxrwx 1 root root 18 Feb 25 2020 /lib32/libreadline.so.8 -> libreadline.so.8.0
-rw-r--r-- 1 root root 311884 Feb 25 2020 /lib32/libreadline.so.8.0
And the relevant part in Makefile is the following:
./configure --prefix=/home/minipc/econet/apps/public/libjson-1.5 --libdir=/lib32 --includedir=/lib32 --disable-static --enable-shared \
And I checked it in the console output when running the make.
So why it still can't find libreadline.so.4? Is it because libreadline.so.8.0 too new to be linked by libreadline.so.4 so the program doesn't recognize it?
Also, when I run
$ ldconfig -p|grep libreadline
libreadline.so.8 (libc6,x86-64) => /lib/x86_64-linux-gnu/libreadline.so.8
libreadline.so.8 (libc6) => /lib32/libreadline.so.8
libreadline.so.5 (libc6,x86-64) => /lib/x86_64-linux-gnu/libreadline.so.5
Only libreadline.so.5 and libreadline.so.4 appears. So the softlink would not be recognized by the system?
The libreadline.so.8 maybe too new to be used as the source of symbolic link of libreadline.so.4. Or it may need to be in another directory such as /lib to be linked by gawk.
I try $gawk return command not found . Then I run $sudo apt install gawk and check the gawk is of version GNU Awk 5.0.1, API: 2.0 (GNU MPFR 4.0.2, GNU MP 6.2.0). I run $make again and found the same error.
Then I try $export $AWKPATH and find out that there is another path to store the gawk bin. Then I enter the directory and run $gawk, the same error pop out. I copy the /usr/bin/gawk ( the newly installed gawk) to update the gawk in the directory, and then run $gawk, it is the newest one.
Then I run $make again and the issue got solved.
Trying to follow this guide: https://plfa.github.io/GettingStarted/
On the part after "Check if the Agda standard library was installed correctly" get this:
$ agda -v 2 nats.agda
Checking nats (C:\Users\AuSeR\agda\nats.agda).
C:\Users\AuSeR\agda\nats.agda:1,1-21
Failed to find source of module Data.Nat in any of the following
locations:
C:\Users\AuSeR\agda\Data\Nat.agda
C:\Users\AuSeR\agda\Data\Nat.lagda
C:\Users\AuSeR\agda\.stack-work\install\5f9701df\share\x86_64-windows-ghc-8.8.3\Agda-2.6.1.1\lib\prim\Data\Nat.agda
C:\Users\AuSeR\agda\.stack-work\install\5f9701df\share\x86_64-windows-ghc-8.8.3\Agda-2.6.1.1\lib\prim\Data\Nat.lagda
when scope checking the declaration
open import Data.Nat
Trying to see the location of libraries file:
$ agda -l fjdsk Dummy.agda
Library 'fjdsk' not found.
Add the path to its .agda-lib file to
'C:\Users\AuSeR\AppData\Roaming\agda\libraries'
to install.
Installed libraries:
(none)
libraries file looks like this:
C:\Users\AuSeR\agda\agda-stdlib\standard-library.agda-lib
defaults like this:
standard-library
I am trying to build and deploy this bookdown project with GitHub Actions. One of the chapters uses the keras R package, which means I need to install Conda (or set up a virtual environment). At the end of the Miniconda installation command, there is an error when trying to collect metadata.
2020-06-24T04:47:59.7495480Z * Miniconda has been successfully installed at '/Users/runner/Library/r-miniconda'.
2020-06-24T04:47:59.7496060Z [1] "/Users/runner/Library/r-miniconda"
2020-06-24T04:48:00.3909040Z * Project '~/runners/2.263.0/work/drake/drake' loaded. [renv 0.10.0]
2020-06-24T04:48:00.7964920Z * The project and lockfile are out of sync -- use `renv::status()` for more details.
2020-06-24T04:48:00.7968340Z Warning message:
2020-06-24T04:48:00.7969190Z Project requested R version '3.6.0' but '4.0.1' is currently being used
2020-06-24T04:48:05.2408080Z Collecting package metadata (current_repodata.json): ...working... failed
2020-06-24T04:48:05.2410390Z
2020-06-24T04:48:05.2410820Z NotWritableError: The current user does not have write permissions to a required path.
2020-06-24T04:48:05.2411080Z path: /usr/local/miniconda/pkgs/cache/b89cf7bf.json
2020-06-24T04:48:05.2411230Z uid: 501
2020-06-24T04:48:05.2411350Z gid: 20
2020-06-24T04:48:05.2411430Z
2020-06-24T04:48:05.2411690Z If you feel that permissions on this path are set incorrectly, you can manually
2020-06-24T04:48:05.2411940Z change them by executing
2020-06-24T04:48:05.2412010Z
2020-06-24T04:48:05.2412260Z $ sudo chown 501:20 /usr/local/miniconda/pkgs/cache/b89cf7bf.json
2020-06-24T04:48:05.2412330Z
2020-06-24T04:48:05.2413470Z In general, it's not advisable to use 'sudo conda'.
2020-06-24T04:48:05.2413570Z
2020-06-24T04:48:05.2414250Z
2020-06-24T04:48:05.2886400Z ##[error]Error: Error 1 occurred creating conda environment r-reticulate
2020-06-24T04:48:05.2890770Z Execution halted
2020-06-24T04:48:05.3050700Z ##[error]Process completed with exit code 1.
The full job log is here.
Depending on how R is set up, this post might be helpful for you. You might need to configure the .Renviron file.
Unable to change python path in reticulate (R)
I have installed a fresh copy of arcanist on to Mac OS X El Capitan (10.11.4) into /usr/local/phabricator/arcanist.
If I first cd into /usr/local/phabricator/arcanist and run either bin/arc or just arc (as I added /usr/local/phabricator/arcanist/bin to my PATH) then all is fine. However if I try and run arc lint from my rocksdb directory on my system then I always get a fatal error, the output looks like this:
$ arc lint --trace
ARGV '/usr/local/phabricator/arcanist/bin/../scripts/arcanist.php' 'lint' '--trace'
LOAD Loaded "phutil" from "/usr/local/phabricator/libphutil/src".
LOAD Loaded "arcanist" from "/usr/local/phabricator/arcanist/src".
Config: Did not find user configuration at "/Users/aretter/.arcrc".
Config: Did not find system configuration at "/etc/arcconfig".
Working Copy: Reading .arcconfig from "/Users/aretter/code/rocksdb/.arcconfig".
Working Copy: Path "/Users/aretter/code/rocksdb" is part of `git` working copy "/Users/aretter/code/rocksdb".
Working Copy: Project root is at "/Users/aretter/code/rocksdb".
Config: Did not find local configuration at "/Users/aretter/code/rocksdb/.git/arc/config".
Loading phutil library from '/Users/aretter/code/rocksdb/arcanist_util'...
[2016-06-14 09:31:17] EXCEPTION: (PhutilMissingSymbolException) Failed to load class or interface 'ArcanistBaseWorkflow': the class or interface 'ArcanistBaseWorkflow' is not defined in the library map for any loaded phutil library.
If you are not a developer, this almost always means that a library is out of date. For example, you may have upgraded `phabricator` without upgrading `libphutil`, or vice versa. It might also mean that you need to restart Apache or PHP-FPM. Make sure all libraries are up to date and all services have been restarted.
If you are a developer and this symbol was recently added or moved, your library map may need to be rebuilt. You can rebuild the map by running 'arc liberate'. For more information, see:
https://secure.phabricator.com/book/phabcontrib/article/adding_new_classes/ at [<phutil>/src/__phutil_library_init__.php:25]
arcanist(head=master, ref.master=c13e5a629535), arcanist_util(head=java-wb-save-restore-points, ref.master=fda098461b3f, ref.java-wb-save-restore-points=dd6d2e75d836), phutil(head=master, ref.master=fb1e159d3640)
#0 __phutil_autoload(string)
#1 spl_autoload_call(string) called at [<arcanist_util>/config/FacebookArcanistConfiguration.php:7]
#2 include_once(string) called at [<phutil>/src/moduleutils/PhutilBootloader.php:226]
#3 PhutilBootloader::executeInclude(string) called at [<phutil>/src/moduleutils/PhutilBootloader.php:216]
#4 PhutilBootloader::loadLibrarySource(string, string) called at [<phutil>/src/symbols/PhutilSymbolLoader.php:381]
#5 PhutilSymbolLoader::loadSymbol(array) called at [<phutil>/src/symbols/PhutilSymbolLoader.php:256]
#6 PhutilSymbolLoader::selectAndLoadSymbols() called at [<phutil>/src/__phutil_library_init__.php:22]
#7 __phutil_autoload(string)
#8 spl_autoload_call(string) called at [<arcanist>/scripts/arcanist.php:186]
Please note that I have tried reinstalling it and also running arc liberate, but neither has fixed the issue.
Can someone tell me what is wrong on my system?
I have also checked with Git that my arcanist is indeed correct and up-to-date:
$ cd /usr/local/phabricator/arcanist
$ git remote -v
origin github.com/phacility/arcanist.git (fetch)
origin github.com/phacility/arcanist.git (push)
$ git status
On branch master Your branch is up-to-date with 'origin/master'. nothing to commit, working directory clean
$ git pull
Already up-to-date.
I also tried reinstalling via this mechanism:
$ cd /usr/local/phabricator
$ rm -rf arcanist libphutil
$ git clone https://github.com/phacility/libphutil.git
$ git clone https://github.com/phacility/arcanist.git
arcanist_util(head=java-wb-save-restore-points, ref.master=fda098461b3f, ref.java-wb-save-restore-points=dd6d2e75d836)
This doesn't look like a fresh copy of arcanist to me from source, at least the upstream isn't responsible for "arcanist_util". Where did you get it from? I would delete it, and pull directly from GitHub. http://github.com/phacility/arcanist