Miniconda3-latest-Linux-x86_64.sh: 494: [[: not found #10431

samuel-hunter · 2020-12-25T23:36:09Z

Current Behavior

After being prompted to run conda init, The miniconda installer exits with the error [[: not found, and then continues installing:

Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
Miniconda3-latest-Linux-x86_64.sh: 494: [[: not found

Steps to Reproduce

Use a Linux distribution that links /bin/sh to a shell outside bash -- Debian, for example. links it to dash.
Download Miniconda3-latest-Linux-x86_64.sh from https://docs.conda.io/en/latest/miniconda.html
Run it either with chmod +x Miniconda3-latest-Linux-x86_64.sh && ./Miniconda3-latest-Linux-x86_64.sh or sh Miniconda3-latest-Linux-x86_64.sh
After being prompted to run conda init, answer yes.

Steps to Fix

It looks like the issue with the command is in the Installer:

# lines 494-499
        if [[ $SHELL = *zsh ]]
        then
            $PREFIX/bin/conda init zsh
        else
            $PREFIX/bin/conda init
        fi

[[, as a bash extension, is not necessarily available for all POSIX shells (as the hashbang #!/bin/sh implies). There are two solutions here:

(Preferred) Replace `[[` with a `case`

# replace lines 494-499 with:
        case $SHELL in
            *zsh)
                $PREFIX/bin/conda init zsh
                ;;
            *)
                $PREFIX/bin/conda init
                ;;
        esac

Explicitly mark the installer as a bash script:

Replace the hashbang on line 1:

-#!/bin/sh
+#!/bin/bash

In theory this solution is easy enough for me to make a pull request instead, but I couldn't for the life of me figure out how the installer is built. acking for the code snippet in this repo shows nothing for me, and being completely new to conda, I don't know which repo out of the 37 in this GitHub organization contains the script that builds the installer. If I could find a pointer to where it is, I'd be happy to set up the pull request.

The text was updated successfully, but these errors were encountered:

aoliong · 2021-07-22T11:54:43Z

Hi, when I fixed the Installer, and change the md5 in Installer, then I got this:

[/project/miniconda3] >>> 
PREFIX=/project/miniconda3
Unpacking payload ...
./Miniconda3-py39_4.9.2-Linux-x86_64.sh: line 412: /project/miniconda3/conda.exe: cannot execute binary file: Exec format error
./Miniconda3-py39_4.9.2-Linux-x86_64.sh: line 414: /project/miniconda3/conda.exe: cannot execute binary file: Exec format error`

How can I fix this ?

I found the solution. The Installer does not need to be modified. Just use this

source activate

samuel-hunter · 2021-07-22T14:08:36Z

Hi @aoliong, it looks like the errors are within lines 412-414. Can you show me a snippet that has those line numbers?

jezdez · 2021-12-16T18:09:22Z

This seems to be an issue in the constructor version that Anaconda uses to build miniconda, which was already fixed in the main repo in https://github.com/conda/constructor/blob/a7ad3d2807129b2cdc596337b5081df1967002d5/constructor/header.sh#L591-L594

jezdez · 2021-12-16T18:12:01Z

I've opened an internal ticket to track the fix.

stmlange · 2022-12-23T07:32:36Z

Any updates on this? This still seems to be a problem with the latest installer:

$ curl -sSL https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o Miniconda3-latest-Linux-x86_64.sh
$ sha256sum *
00938c3534750a0e4069499baf8f4e6dc1c2e471c86a59caa0dd03f4a9269db6  Miniconda3-latest-Linux-x86_64.sh
$ chmod +x Miniconda3-latest-Linux-x86_64.sh
$ ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3

fails with

./Miniconda3-latest-Linux-x86_64.sh: 438: [[: not found
./Miniconda3-latest-Linux-x86_64.sh: 444: [[: not found

Thanks!

AnkushMalaker · 2022-12-23T08:40:10Z

I'm facing the same issue with the py39 installer as-well.
I get the following logs:

PREFIX=/home/ubuntu/miniconda3
Unpacking payload ...
                                                                                                         
Installing base environment...


Downloading and Extracting Packages


Downloading and Extracting Packages

Preparing transaction: done
Executing transaction: done
Miniconda3-latest-Linux-x86_64.sh: 438: [[: not found

Installing * environment...

Miniconda3-latest-Linux-x86_64.sh: 444: [[: not found

CondaFileIOError: '/home/ubuntu/miniconda3/pkgs/envs/*/env.txt'. [Errno 2] No such file or directory: '/home/ubuntu/miniconda3/pkgs/envs/*/env.txt'

This is a fresh install of ubuntu 22.10.

Edit: This issue for me was caused because I was using sh to execute the installer instead of bash.
Using bash Miniconda3-latest-Linux-x86_64.sh to install worked.
@stmlange Could you try the same?

stmlange · 2022-12-23T08:59:12Z

Thanks for the hint! I was initially trying the source activate which was suggested in one of the previous comments which didn't work. Using bash Miniconda3-latest-Linux-x86_64.sh to install works fine on ubuntu jammy (22.04.1 LTS).

jonhermansen · 2022-12-23T17:36:14Z

I ran into this issue today as well, thank you all for the suggestion of running under bash

Perhaps the shebang at the top of the script, should be changed?

dbast · 2022-12-23T19:51:14Z

related conda/constructor#596

ezyang · 2022-12-24T07:07:42Z

This is more pressing now that focal is shipping a sh that doesn't understand this bash-ism

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyang@fb.com> [ghstack-poisoned]

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyangfb.com> ghstack-source-id: 38cc3d169355f973974fac918ba6c18808454227 Pull Request resolved: #91371

pat-s · 2022-12-25T08:56:25Z

I also just hit this in focal latest. Quite unfortunate from an outside perspective.

Invoking the .sh script with ./ should really work as one rarely calls bash <script>.sh in an automation workflow. A working shebang definition should solve this.

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyang@fb.com> Pull Request resolved: #91371 Approved by: https://github.com/albanD

…rict POSIX sh" See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyangfb.com> [ghstack-poisoned]

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyangfb.com> [ghstack-poisoned]

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyangfb.com> ghstack-source-id: 9a39ea1c200e633cc96a1cd12867cc4d835e4b97 Pull Request resolved: #91371

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyang@fb.com> Pull Request resolved: #91371 Approved by: https://github.com/albanD

stmlange · 2022-12-28T15:53:41Z

Thanks for your quick reaction and fix despite the fact that I have re-used an old issue in the wrong repo (for me it wasn't clear where to report it and this one was still open) :-)

sbrozell · 2022-12-29T22:38:11Z

Thanks. When will the fix go live ?

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyang@fb.com> Pull Request resolved: pytorch#91371 Approved by: https://github.com/albanD

sbrozell · 2023-01-04T21:33:07Z

Is it expected that this will ultimately be fixed in release distribution ?

Fixes the issue caused by conda/conda#10431 by including mithro/make-env#31 Signed-off-by: Tim 'mithro' Ansell <tansell@google.com>

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyang@fb.com> Pull Request resolved: pytorch#91371 Approved by: https://github.com/albanD

The Minconda installer seems to expect that `[[` can be used in all sh implementations, which is not necessarily the case (there are some discussions around this issue e.g. in conda/conda#10431). To attempt to work around this, we run the installer with bash instead.

donaldafeith · 2023-01-17T01:57:31Z

Remember to restart. (I'm running WSL 2 and was able to install it by)

curl -sSL https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh -b -p /home/user/miniconda3a **because I have windows python installed with miniconda /user/miniconda3
conda config --set auto_activate_base false
exited out of WSL2
Restarted WSL2
conda --version

divinity76 · 2023-01-20T02:31:08Z

seems to still be unfixed as of 2023-01-20, and the bash -c workaround does NOT work, i can reproduce it with this Dockerfile:

FROM ubuntu:22.04
ENV DEBIAN_FRONTEND=noninteractive 
RUN apt-get update -y
RUN apt-get install -y wget
RUN wget --no-verbose 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh';
RUN chmod +x ./Miniconda3-latest-Linux-x86_64.sh;
RUN bash -c './Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda;'

yields

$ docker build -f Dockerfile .;
Sending build context to Docker daemon  92.34MB
Step 1/28 : FROM ubuntu:22.04
 ---> 6b7dfa7e8fdb
Step 2/28 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 9fcfd668e8a3
Step 3/28 : RUN apt-get update -y
 ---> Using cache
 ---> 76449545c502
Step 4/28 : RUN apt-get install -y wget
 ---> Using cache
 ---> 5c0ab313726e
Step 5/28 : RUN wget --no-verbose 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh';
 ---> Running in 763122d8236d
2023-01-20 02:29:04 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [72402405/72402405] -> "Miniconda3-latest-Linux-x86_64.sh" [1]
Removing intermediate container 763122d8236d
 ---> aa1dcca06d6f
Step 6/28 : RUN chmod +x ./Miniconda3-latest-Linux-x86_64.sh;
 ---> Running in 06dec8f155ac
Removing intermediate container 06dec8f155ac
 ---> 333dd872b5e3
Step 7/28 : RUN bash -c './Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda;'
 ---> Running in 85b760c4cf22
PREFIX=/miniconda
Unpacking payload ...
                                                                                                               
Installing base environment...


Downloading and Extracting Packages


Downloading and Extracting Packages

Preparing transaction: ...working... done
Executing transaction: ...working... done
./Miniconda3-latest-Linux-x86_64.sh: 438: [[: not found

Installing * environment...

./Miniconda3-latest-Linux-x86_64.sh: 444: [[: not found

CondaFileIOError: '/miniconda/pkgs/envs/*/env.txt'. [Errno 2] No such file or directory: '/miniconda/pkgs/envs/*/env.txt'

The command '/bin/sh -c bash -c './Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda;'' returned a non-zero code: 1

dbast · 2023-01-20T08:00:29Z

you have to call bash Miniconda3-latest-Linux-x86_64.sh ... without -c ... and also no need for the chmod call!

divinity76 · 2023-01-21T00:17:23Z

@dbast that actually worked! thanks! btw i'm positive there is a bug in the current Miniconda3-latest-Linux-x86_64.sh where it uses #!/bin/bash-exclusive syntax with the shebang #!/bin/sh , causing normal invocation to crash, but when the file is invoked with bash Miniconda...sh , the shebang will be ignored, and it will be parsed with bash-rules regardless of shebang~

Aemon-Algiz · 2023-05-22T00:45:45Z

@divinity76 You are a hero.

chenghlee added the source::community catch-all for issues filed by community members label Jan 7, 2021

csmcal referenced this issue in MesserLab/SLiM-Extras Jan 25, 2021

try adding the -j$(nproc) flag to make; remove "\n"

2c4b5f9

mausch mentioned this issue Apr 2, 2021

miniconda installer script uses bash's extended test command but specifies sh as shebang #10566

Closed

chenghlee added the type::installer indicates a request or issue pertaining to the installer label Apr 10, 2021

chenghlee added this to the Release TBD milestone Apr 10, 2021

kenodegard removed this from the Release TBD milestone Dec 3, 2021

conda-bot added the backlog issue has been triaged but has not been earmarked for any upcoming release label Dec 3, 2021

jezdez added the severity::2 critical; broken functionality with an unacceptably complex workaround label Dec 16, 2021

ezyang mentioned this issue Dec 24, 2022

Fix conda install on distributions with strict POSIX sh pytorch/pytorch#91371

Closed

ezyang added a commit to pytorch/pytorch that referenced this issue Dec 24, 2022

Fix conda install on distributions with strict POSIX sh

eede6b1

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyang@fb.com> [ghstack-poisoned]

coolbreeze413 mentioned this issue Dec 26, 2022

add fifo & ram macros, add specify block from ram and fifos chipsalliance/yosys-f4pga-plugins#415

Merged

chainsawriot mentioned this issue Dec 27, 2022

Linux/OSX: install_miniconda has a hidden assumption of requiring /bin/sh links to bash rstudio/reticulate#1306

Closed

pytorchmergebot pushed a commit to pytorch/pytorch that referenced this issue Dec 28, 2022

Update base for Update on "Fix conda install on distributions with st…

e572a97

…rict POSIX sh" See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyangfb.com> [ghstack-poisoned]

pytorchmergebot pushed a commit to pytorch/pytorch that referenced this issue Dec 28, 2022

Update on "Fix conda install on distributions with strict POSIX sh"

8a925e0

See also conda/conda#10431 Signed-off-by: Edward Z. Yang <ezyangfb.com> [ghstack-poisoned]

jaimergp mentioned this issue Dec 28, 2022

make shell installers POSIX compliant conda/constructor#599

Merged

3 tasks

dbast mentioned this issue Dec 28, 2022

Miniconda installer script declared as #!/bin/sh but syntax is bash conda/conda-docs#836

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suchenzang mentioned this issue Dec 30, 2022

Fix circleci: use bash facebookresearch/metaseq#575

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Update to v0.5 eco4cast/EFIstandards#34

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Installation fails using sh #12207

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Ci fixes RTimothyEdwards/open_pdks#338

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mithro added a commit to mithro/skywater-pdk that referenced this issue Jan 7, 2023

Update make-env submodule.

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Fixes the issue caused by conda/conda#10431 by including mithro/make-env#31 Signed-off-by: Tim 'mithro' Ansell <tansell@google.com>

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Update make-env submodule. google/skywater-pdk#408

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Miniconda3-latest-Linux-x86_64.sh: 494: [[: not found #10431

Miniconda3-latest-Linux-x86_64.sh: 494: [[: not found #10431

samuel-hunter commented Dec 25, 2020 •

edited by kenodegard

aoliong commented Jul 22, 2021 •

edited

samuel-hunter commented Jul 22, 2021

jezdez commented Dec 16, 2021

jezdez commented Dec 16, 2021

stmlange commented Dec 23, 2022 •

edited

AnkushMalaker commented Dec 23, 2022 •

edited

stmlange commented Dec 23, 2022

jonhermansen commented Dec 23, 2022

dbast commented Dec 23, 2022

ezyang commented Dec 24, 2022

pat-s commented Dec 25, 2022

stmlange commented Dec 28, 2022

sbrozell commented Dec 29, 2022

sbrozell commented Jan 4, 2023

donaldafeith commented Jan 17, 2023

divinity76 commented Jan 20, 2023

dbast commented Jan 20, 2023

divinity76 commented Jan 21, 2023

Aemon-Algiz commented May 22, 2023

Miniconda3-latest-Linux-x86_64.sh: 494: [[: not found #10431

Miniconda3-latest-Linux-x86_64.sh: 494: [[: not found #10431

Comments

samuel-hunter commented Dec 25, 2020 • edited by kenodegard

Current Behavior

Steps to Reproduce

Steps to Fix

(Preferred) Replace [[ with a case

Explicitly mark the installer as a bash script:

aoliong commented Jul 22, 2021 • edited

samuel-hunter commented Jul 22, 2021

jezdez commented Dec 16, 2021

jezdez commented Dec 16, 2021

stmlange commented Dec 23, 2022 • edited

AnkushMalaker commented Dec 23, 2022 • edited

stmlange commented Dec 23, 2022

jonhermansen commented Dec 23, 2022

dbast commented Dec 23, 2022

ezyang commented Dec 24, 2022

pat-s commented Dec 25, 2022

stmlange commented Dec 28, 2022

sbrozell commented Dec 29, 2022

sbrozell commented Jan 4, 2023

donaldafeith commented Jan 17, 2023

divinity76 commented Jan 20, 2023

dbast commented Jan 20, 2023

divinity76 commented Jan 21, 2023

Aemon-Algiz commented May 22, 2023

samuel-hunter commented Dec 25, 2020 •

edited by kenodegard

(Preferred) Replace `[[` with a `case`

aoliong commented Jul 22, 2021 •

edited

stmlange commented Dec 23, 2022 •

edited

AnkushMalaker commented Dec 23, 2022 •

edited