Issues when attempting to build latest version

[jstnlvns]

Justin Levens from University of Kentucky

I'm having trouble building the latest version, here are the errors before it exits the build:

Using: ~/quip_distro$ docker-compose -f quip-pathdb.yml build

Step 1/25 : FROM ubuntu:bionic
 ---> ad080923604a
Step 2/25 : LABEL maintainer="[email protected]"
 ---> Using cache
 ---> aafd953836bf
Step 3/25 : RUN echo "Start update"
 ---> Using cache
 ---> 5e04846eee68
Step 4/25 : RUN   sed -i 's/# \(.*multiverse$\)/\1/g' /etc/apt/sources.list &&   apt-get update &&   apt-get -y upgrade
 ---> Using cache
 ---> e19519bfd13d
Step 5/25 : RUN   apt-get install -y libcurl4 openssl &&   apt-get install -y build-essential &&   apt-get install -y software-properties-common &&   apt-get install -y byobu curl git htop man unzip vim wget gnupg
 ---> Using cache
 ---> 2cf3b52e1681
Step 6/25 : RUN echo "Install Mongo and Node"
 ---> Using cache
 ---> 2e517a82dcc2
Step 7/25 : RUN echo "deb [ arch=amd64 ] http://repo.mongodb.org/apt/ubuntu bionic/mongodb-org/4.0 multiverse" | tee /etc/apt/sources.list.d/mongodb-org-4.0.list
 ---> Using cache
 ---> 5cd11fae91cf
Step 8/25 : RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 68818C72E52529D4
 ---> Running in 33fed5a59567
Warning: apt-key output should not be parsed (stdout is not a terminal)
Executing: /tmp/apt-key-gpghome.bDSDL82pNJ/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 68818C72E52529D4
gpg: keyserver receive failed: End of file
The command '/bin/sh -c apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 68818C72E52529D4' returned a non-zero code: 2
ERROR: Service 'heatmaploader' failed to build

I updated docker-compose to the latest version (Docker Compose version v2.7.0) because I was running an older version, but had the same result:

$ docker-compose -f quip-pathdb.yml build
[+] Building 228.3s (50/111)                                                                                                                                                                                         
 => [quip_distro_segloader internal] load git source https://github.com/SBU-BMI/SegmentationLoader.git#2.1                                                                                                      1.1s
 => [quip_distro_imageloader internal] load git source https://github.com/SBU-BMI/ImageLoader.git#2.1.1                                                                                                        15.8s
 => [quip_distro_heatmaploader internal] load git source https://github.com/SBU-BMI/uploadHeatmaps.git#v1.5.4                                                                                                   1.2s
 => [quip_distro_back internal] load git source https://github.com/camicroscope/caracal.git#v3.9.10                                                                                                             1.4s
 => [quip_distro_pathdb internal] load git source https://github.com/SBU-BMI/PathDB.git#1.7.1                                                                                                                  18.1s
 => [quip_distro_segloader internal] load metadata for docker.io/library/mongo:latest                                                                                                                           0.0s
 => [quip_distro_segloader  1/10] FROM docker.io/library/mongo:latest                                                                                                                                           0.7s
 => [quip_distro_heatmaploader internal] load metadata for docker.io/library/ubuntu:bionic                                                                                                                      0.0s
 => [quip_distro_heatmaploader  1/21] FROM docker.io/library/ubuntu:bionic                                                                                                                                      0.1s
 => [quip_distro_heatmaploader  2/21] RUN echo "Start update"                                                                                                                                                   0.8s
 => [quip_distro_back internal] load metadata for docker.io/library/node:16-stretch-slim                                                                                                                        0.0s
 => [quip_distro_back 1/8] FROM docker.io/library/node:16-stretch-slim                                                                                                                                          0.4s
 => [quip_distro_segloader  2/10] RUN apt-get upgrade && apt-get update && apt-get install -y wget git vim build-essential checkinstall                                                                       122.4s
 => [quip_distro_back 2/8] RUN apt-get update  &&  apt-get upgrade -y  &&  apt-get install -y git build-essential python3                                                                                     142.6s 
 => [quip_distro_heatmaploader  3/21] RUN   sed -i 's/# \(.*multiverse$\)/\1/g' /etc/apt/sources.list &&   apt-get update &&   apt-get -y upgrade                                                              43.2s 
 => [quip_distro_imageloader internal] load metadata for docker.io/library/ubuntu:18.04                                                                                                                         0.0s 
 => [quip_distro_imageloader  1/14] FROM docker.io/library/ubuntu:18.04                                                                                                                                         0.0s 
 => [quip_distro_imageloader  2/14] RUN apt-get update                                                                                                                                                         20.1s 
 => [quip_distro_pathdb internal] load metadata for docker.io/library/centos:7                                                                                                                                  0.0s 
 => [quip_distro_pathdb  1/48] FROM docker.io/library/centos:7                                                                                                                                                  0.4s
 => [quip_distro_pathdb  2/48] RUN yum update -y && yum clean all                                                                                                                                             157.4s
 => [quip_distro_imageloader  3/14] RUN apt-get install -y wget                                                                                                                                                21.1s
 => [quip_distro_heatmaploader  4/21] RUN   apt-get install -y libcurl4 openssl &&   apt-get install -y build-essential &&   apt-get install -y software-properties-common &&   apt-get install -y byobu cur  178.6s
 => [quip_distro_imageloader  4/14] RUN wget https://download.java.net/java/GA/jdk12.0.2/e482c34c86bd4bf8b56c0b35558996b9/10/GPL/openjdk-12.0.2_linux-x64_bin.tar.gz                                           16.3s
 => [quip_distro_imageloader  5/14] RUN tar xvfz openjdk-12.0.2_linux-x64_bin.tar.gz                                                                                                                           16.3s
 => [quip_distro_imageloader  6/14] RUN mkdir /usr/java                                                                                                                                                         0.9s
 => [quip_distro_imageloader  7/14] RUN mv jdk-12.0.2 /usr/java                                                                                                                                                10.5s
 => [quip_distro_imageloader  8/14] RUN ln -s /usr/java/jdk-12.0.2/bin/java /usr/bin/java                                                                                                                       1.1s
 => [quip_distro_imageloader  9/14] COPY run.sh /root                                                                                                                                                           0.3s
 => [quip_distro_imageloader 10/14] COPY *.jar /usr/bin                                                                                                                                                         1.2s
 => [quip_distro_imageloader 11/14] COPY imageloader /usr/bin                                                                                                                                                   0.3s
 => [quip_distro_imageloader 12/14] COPY maploader /usr/bin                                                                                                                                                     0.3s
 => [quip_distro_imageloader 13/14] RUN chmod 0755 /usr/bin/imageloader                                                                                                                                         1.1s
 => [quip_distro_imageloader 14/14] RUN chmod 0755 /usr/bin/maploader                                                                                                                                           1.0s
 => [quip_distro_imageloader] exporting to image                                                                                                                                                               10.8s
 => => exporting layers                                                                                                                                                                                        10.8s
 => => writing image sha256:115b5c681bb0351932e38ab120392c8a296810ddc8db7a4187a6d25985e6cccc                                                                                                                    0.0s
 => => naming to docker.io/library/quip_distro_imageloader                                                                                                                                                      0.0s 
 => [quip_distro_segloader  3/10] RUN apt-get install -y libreadline-gplv2-dev libncursesw5-dev libssl-dev     libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev libffi-dev zlib1g-dev                    90.2s 
 => [quip_distro_back 3/8] RUN mkdir /src                                                                                                                                                                       0.8s 
 => [quip_distro_back 4/8] COPY . /src                                                                                                                                                                          0.3s 
 => [quip_distro_back 5/8] WORKDIR /src                                                                                                                                                                         0.3s 
 => [quip_distro_back 6/8] RUN npm install                                                                                                                                                                     36.4s 
 => [quip_distro_pathdb  3/48] RUN yum -y install wget which zip unzip bind-utils epel-release                                                                                                                 25.5s 
 => [quip_distro_back 7/8] RUN git clone https://github.com/${fork:-camicroscope}/camicroscope.git --branch=v3.9.10                                                                                            16.9s
 => CANCELED [quip_distro_back 8/8] RUN chgrp -R 0 /src &&     chmod -R g+rwX /src                                                                                                                             28.5s 
 => [quip_distro_pathdb  4/48] RUN rpm -Uvh http://mirror.bebout.net/remi/enterprise/remi-release-7.rpm                                                                                                         2.1s 
 => [quip_distro_pathdb  5/48] RUN yum-config-manager --enable remi-php73                                                                                                                                       2.1s 
 => CANCELED [quip_distro_pathdb  6/48] RUN yum -y install httpd openssl mod_ssl mod_php php-opcache php-xml php-mcrypt php-gd php-devel php-mysql php-intl php-mbstring php-uploadprogress php-pecl-zip php-  21.8s 
 => CANCELED [quip_distro_segloader  4/10] RUN cd /usr/src && wget https://www.python.org/ftp/python/3.7.3/Python-3.7.3.tgz && tar xzf Python-3.7.3.tgz && cd Python-3.7.3 && ./configure --enable-optimizati  13.7s 
 => [quip_distro_heatmaploader  5/21] RUN echo "Install Mongo and Node"                                                                                                                                         1.0s 
 => [quip_distro_heatmaploader  6/21] RUN echo "deb [ arch=amd64 ] http://repo.mongodb.org/apt/ubuntu bionic/mongodb-org/4.0 multiverse" | tee /etc/apt/sources.list.d/mongodb-org-4.0.list                     1.1s 
 => ERROR [quip_distro_heatmaploader  7/21] RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 68818C72E52529D4                                                                                       1.4s 
------                                                                                                                                                                                                               
 > [quip_distro_heatmaploader  7/21] RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 68818C72E52529D4:                                                                                                  
#0 0.944 Warning: apt-key output should not be parsed (stdout is not a terminal)                                                                                                                                     
#0 1.022 Executing: /tmp/apt-key-gpghome.ZB5dbdOqdD/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 68818C72E52529D4                                                                                           
#0 1.215 gpg: keyserver receive failed: End of file                                                                                                                                                                  
------                                                                                                                                                                                                               
failed to solve: executor failed running [/bin/sh -c apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 68818C72E52529D4]: exit code: 2

[birm]

Hello, and thank you for reporting. I have not yet been able to replicate this issue, but I've seen similar issues arising from network or firewall configuration.
While I can't help you there, I can advise that you may want to use the docker image I have built, from https://hub.docker.com/r/camicroscope/pathdb-heatmaploader
To do that, in the compose file, change "build" to "image" and its value to "camicroscope/pathdb-heatmaploader"
Please let me know if this resolves your issue.