POM errors while building Prokaryote with Maven 3.5.0

[oleksandr-pavlyk]

On a machine with Oracle Java 1.8 installed, and using Miniconda python installation, I create an environment to build prokaryote:

conda create -n _b_prokaryote python setuptools maven --yes
source _b_prokaryote

Then, I clone CellProfiler/prokaryote repo, and while using revision cfeb877 execute mvn clean package. I get the following error:

(_b_prokaryote) [11:51:46 fxsatlin04 prokaryote]$ mvn clean package
[INFO] Scanning for projects...
Downloading: https://oss.sonatype.org/content/repositories/releases/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://maven.imagej.net/content/groups/public/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://artifacts.openmicroscopy.org/artifactory/ome.releases/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://artifacts.openmicroscopy.org/artifactory/ome.snapshots/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://artifacts.openmicroscopy.org/artifactory/springsource-release/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/bundles/release/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/bundles/external/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/libraries/release/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/libraries/external/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: https://repo.maven.apache.org/maven2/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
[ERROR] [ERROR] Some problems were encountered while processing the POMs:
[FATAL] Non-resolvable parent POM for org.cellprofiler:prokaryote:2.3.0: Could not transfer artifact org.scijava:pom-scijava:pom:10.4.1 from/to sonatype-nexus-releases (https://oss.sonatype.org/content/repositories/releases): Connect to oss.sonatype.org:443 [oss.sonatype.org/107.23.166.173, oss.sonatype.org/34.199.111.237] failed: Connection timed out (Connection timed out) and 'parent.relativePath' points at wrong local POM @ line 245, column 13
 @ 
[ERROR] The build could not read 1 project -> [Help 1]
[ERROR]   
[ERROR]   The project org.cellprofiler:prokaryote:2.3.0 (/localdisk/work/opavlyk/projects/cellprofiler/sources/prokaryote/pom.xml) has 1 error
[ERROR]     Non-resolvable parent POM for org.cellprofiler:prokaryote:2.3.0: Could not transfer artifact org.scijava:pom-scijava:pom:10.4.1 from/to sonatype-nexus-releases (https://oss.sonatype.org/content/repositories/releases): Connect to oss.sonatype.org:443 [oss.sonatype.org/107.23.166.173, oss.sonatype.org/34.199.111.237] failed: Connection timed out (Connection timed out) and 'parent.relativePath' points at wrong local POM @ line 245, column 13 -> [Help 2]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
[ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException

The conda environment I used:

(_b_prokaryote) [12:20:44 fxsatlin04 prokaryote]$ conda list --explicit
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://repo.continuum.io/pkgs/free/linux-64/certifi-2016.2.28-py36_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/maven-3.5.0-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/openjdk-8.0.121-1.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/openssl-1.0.2l-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/pip-9.0.1-py36_1.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/python-3.6.2-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/readline-6.2-2.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/setuptools-36.4.0-py36_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/sqlite-3.13.0-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/tk-8.5.18-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/wheel-0.29.0-py36_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/xz-5.2.3-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/zlib-1.2.11-0.tar.bz2

I noticed that Travis is using an older version of Maven, specifically 3.3.9, but I am not sure if it the version of Maven that is the problem.

Please advise.

[chris-allan]

Now that 2.3.2 has been released I would check to see if this issue has been resolved. Several problems with the POM were fixed. I don't have any issues running clean package with Maven 3.3.9 or 3.5.2 at the moment.

[ctrueden]

Connect to oss.sonatype.org:443 [oss.sonatype.org/107.23.166.173, oss.sonatype.org/34.199.111.237] failed: Connection timed out (Connection timed out)

☝️ Implies to me it was a temporary connectivity issue, probably not specific to the version of Maven used? I suggest closing this.