Network Issues During Installation

Problem Description

When attempting to install chromIDEAS using the command:

conda install fatyang::chromideas

The process gets stuck at the following stage:

Screenshot showing stalled conda installation

Root Cause

This issue typically occurs due to poor network connectivity, which is more common in certain regions (such as China).

Solution

To resolve this, manually download the GenomeInfoDbData_1.2.13.tar.gz package to bypass conda’s repeated download attempts.

Procedure:

  1. Press Ctrl + C to terminate the installation process.

  2. Manually download the GenomeInfoDbData_1.2.13.tar.gz package (highlighted in yellow in the screenshot) and upload it to the server location shown in red:

    /share/home/fatyang/Micromamba/envs/sra/share/genomeinfodbdata-1.2.13/

    Ensure the filename is exactly "GenomeInfoDbData_1.2.13.tar.gz", not GenomeInfoDbData_1.2.13.tar.gz.

  3. Modify the installation script. Edit the installBiocDataPackage.sh script (highlighted in green) by adding the following three lines as indicated:

    #!/bin/bash
set -ex
# takes a single parameter, the package name

SCRIPT_DIR="$( dirname -- "${BASH_SOURCE[0]}" )/../share/bioconductor-data-packages"
json="${SCRIPT_DIR}/dataURLs.json"
FN=`yq ".\"$1\".fn" "${json}"`
##readarray is bash4, while OSX only has bash 3
#readarray URLS < <(yq ".\"$1\".urls[]" "${json}")
while IFS= read -r value; do
        URLS+=($value);
done < <(yq ".\"$1\".urls[]" "${json}")
MD5=`yq ".\"$1\".md5" "${json}"`

# Use a staging area in the conda dir rather than temp dirs, both to avoid
# permission issues as well as to have things downloaded in a predictable
# manner.
STAGING=$PREFIX/share/"$1"
mkdir -p $STAGING
TARBALL=$STAGING/$FN

SUCCESS=0
for URL in ${URLS[@]}; do
        URL=`echo $URL | tr -d \"`  # Trim any flanking quotes
        MD5=`echo $MD5 | tr -d \"`  # Trim any flanking quotes

#################################### add by fatyang ####################################
        if [[ ! -f ${TARBALL} ]]; then
                curl -L $URL > $TARBALL
        fi
#################################### add by fatyang ####################################
        [[ $? == 0 ]] || continue

        # Platform-specific md5sum checks.
        if [[ $(uname -s) == "Linux" ]]; then
                if md5sum -c <<<"$MD5  $TARBALL"; then
                        SUCCESS=1
                        break
                fi
        else if [[ $(uname -s) == "Darwin" ]]; then
                if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then
                        SUCCESS=1
                        break
                fi
        fi
fi
done

if [[ $SUCCESS != 1 ]]; then
        echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:"
        printf '%s\n' "${URLS[@]}"
        exit 1
fi

# Install and clean up
R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL
rm $TARBALL
rmdir $STAGING

  4. Re-run the installation command:

    conda install fatyang::chromideas

    The installation should now complete successfully.

Additional Support

If you encounter further issues while using chromIDEAS: