BUG(cran) - Unable to install python or R packages in credo environment

[kendomaniac]

From a Mac M4 I downloaded an arm64 ubuntu docker.
In the ubuntu, I have installed python latest version and pip. I also installed R and R-dev
I downloaded the credo release for linux arm64.
If I try to install numpy:
./credo pip numpy I get thi error
2025/03/12 15:25:17 pip.go:235: bareRun, retrieving pip binary: getPipBinary, setting up venv: exit status 1
If I try to install 'Seurat' CRAN package: ./credo cran 'Seurat'
I get this error:
2025/03/12 14:50:44 cran.go:284: [cran] run: exit status 1

The docker can be retrieve as docker pull repbioinfo/testing_credo:arm64

[eliseomartelli]

Is it possible for you to try to create an image with this minimal Dockerfile?

FROM ubuntu:24.04 AS base

ENV \
    DEBIAN_FRONTEND=noninteractive \
    LANG="C.UTF-8"

SHELL ["/bin/bash", "-o", "pipefail", "-c"]

FROM base AS builder

WORKDIR /

ARG CREDO_VERSION="v0.13.4"
ARG CREDO_ARCH="arm64"
ARG CREDO_URL="https://github.com/CREDOProject/core/releases/download/${CREDO_VERSION}/linux_${CREDO_ARCH}_credo.zip"

RUN set -x \
    && apt-get update -yq --no-install-recommends \
    && apt-get install -yq --no-install-recommends \
    ca-certificates \
    curl \
    unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && curl -fsSL --proto '=https' --tlsv1.2 "${CREDO_URL}" -o credo.zip \
    && unzip credo.zip \
    && rm -f credo.zip \
    && chmod +x credo

FROM base AS final

RUN set -x \
    && apt-get update -yq --no-install-recommends \
    && apt-get install -yq --no-install-recommends \
    build-essential \
    r-base \
    python3 \
    python3-pip \
    python3-virtualenv \
    gfortran \
    ca-certificates \
    && apt-get clean

COPY --from=builder /credo /usr/bin/credo

WORKDIR /workdir

Let me know if that works for you.

[kendomaniac]

I dit it and running in /workingdir
credo pip numpy I got this error:
root@60d5d73d5479:/workdir# credo pip numpy
2025/03/12 15:36:20 pip.go:235: bareRun, retrieving pip binary: getPipBinary, setting up venv: exit status 1

I repeated the building on linux server using amd64 version of credo and I get the same error:
root@80ffd2867132:/workdir# credo pip numpy
2025/03/12 15:43:18 pip.go:235: bareRun, retrieving pip binary: getPipBinary, setting up venv: exit status 1
root@80ffd2867132:/workdir#