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mintUpdate does not update libgdal-dev from ppa:ubuntugis/ubuntugis-unstable #716

Closed florisvdh closed 1 year ago

florisvdh commented 2 years ago

Describe the bug

Each time that an update becomes available of the libgdal-dev package at ppa:ubuntugis/ubuntugis-unstable, it is not updated by mintUpdate. mintUpdate considers everything up to date after other installed packages from the same PPA were updated, such as gdal-bin and gdal-data. As a result, libgdal-dev can still be seen in apt list --upgradable output (hence needs to be manually updated on the command line):

$ apt list --upgradable | grep gdal
libgdal-dev/focal 3.4.0+dfsg-1~focal0 amd64 [upgradable from: 3.3.2+dfsg-2~focal2]
$ 
$ apt policy libgdal-dev
libgdal-dev:
  Installed: 3.3.2+dfsg-2~focal2
  Candidate: 3.4.0+dfsg-1~focal0
  Version table:
     3.4.0+dfsg-1~focal0 500
        500 http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu focal/main amd64 Packages
 *** 3.3.2+dfsg-2~focal2 100
        100 /var/lib/dpkg/status
     3.0.4+dfsg-1build3 500
        500 http://ftp.belnet.be/ubuntu focal/universe amd64 Packages

I did not blacklist the package in mintUpdate nor hold the package with dpkg --set-selections. I saw the same happening at least during the previous update, i.e. multiple months ago.

To Reproduce

Steps to reproduce the behavior:

  1. Add ppa:ubuntugis/ubuntugis-unstable
  2. Install libgdal-dev
  3. Wait for a next version to appear on the PPA.
  4. Observe that libgdal-dev is not updated, contrary to e.g. gdal-bin and gdal-data

Expected behavior

libgdal-dev is updated together with the other GDAL packages that were updated at the PPA.

Distribution:

Software version:

5.7.8 (on Linux Mint 20 Cinnamon)

Additional context

Could it be related with the package appearing under the main/g/gdal directory (URL), not under main/libg while the package name starts with 'libg'?

Anyhow, it poses no problem with apt, but some reason makes mintUpdate miss the package.

The PPA-list of packages under 'gdal' can also be consulted here, by expanding the first hit (gdal - 3.4.0+dfsg-1~focal0).

clefebvre commented 2 years ago

Can you run:

/usr/lib/linuxmint/mintUpdate/checkAPT.py

florisvdh commented 2 years ago 
$ /usr/lib/linuxmint/mintUpdate/checkAPT.py
b"###foreign###foreign###foreign###foreign=0.8.82-1.2004.0###r-cran-foreign###r-cran-foreign###0.8.82-1.2004.0###0.8.81-1.2004.0###238344###package###CRAN###GNU R package to read/write data from other stat. systems###This package provides functions for reading and writing data stored by statistical packages such as Minitab, S, SAS, SPSS, Stata, ...\n\nThis package is part of the set of packages that are 'recommended' by R Core and shipped with upstream source releases of R itself.###cloud.r-project.org###focal-cran40---EOL---"
b'###Linux kernel 5.13.0.25.26~20.04.12###linux-5.13.0.25.26~20.04.12###linux-meta-hwe-5.13###linux-meta-hwe-5.13=5.13.0.25.26~20.04.12###linux-headers-generic-hwe-20.04###linux-headers-generic-hwe-20.04, linux-image-generic-hwe-20.04, linux-generic-hwe-20.04###5.13.0.25.26~20.04.12###5.11.0.46.51~20.04.23###7040###kernel###ubuntu###The Linux kernel###The Linux Kernel is responsible for hardware and drivers support. Note that this update will not remove your existing kernel. You will still be able to boot with the current kernel by choosing the advanced options in your boot menu. Please be cautious though.. kernel regressions can affect your ability to connect to the Internet or to log in graphically. DKMS modules are compiled for the most recent kernels installed on your computer. If you are using proprietary drivers and you want to use an older kernel, you will need to remove the new one first.###ftp.belnet.be###focal-updates---EOL---'
b"###r-cran-class###r-cran-class###r-cran-class###r-cran-class=7.3-20-1.2004.0###r-cran-class###r-cran-class###7.3-20-1.2004.0###7.3-19-1.2004.0###87796###package###CRAN###GNU R package for classification###The class package provides functions and datasets to support chapter 12 on 'Classification' in the book 'Modern Applied Statistics with S' (4th edition) by W.N. Venables and B.D. Ripley. The following URL provides more details about the book: URL: http://www.stats.ox.ac.uk/pub/MASS4###cloud.r-project.org###focal-cran40---EOL---"
b"###nlme###nlme###nlme###nlme=3.1.155-1.2004.0###r-cran-nlme###r-cran-nlme###3.1.155-1.2004.0###3.1.152-1.2004.0###2233932###package###CRAN###GNU R package for (non-)linear mixed effects models###This package provides functions to fit and compare linear and non-linear mixed-effects models.\n\nThis package is part of the set of packages that are 'recommended' by R Core and shipped with upstream source releases of R itself.###cloud.r-project.org###focal-cran40---EOL---"
b"###r-cran-nnet###r-cran-nnet###r-cran-nnet###r-cran-nnet=7.3-17-1.2004.0###r-cran-nnet###r-cran-nnet###7.3-17-1.2004.0###7.3-16-1.2004.0###111656###package###CRAN###GNU R package for feed-forward neural networks###The nnet package provides functions and datasets to support feed-forward neural networks with a single hidden layer, and multinomial log-linear models, as discussed in the book 'Modern Applied Statistics with S' (4th edition) by W.N. Venables and B.D. Ripley. The following URL provides more details about the book: URL: http://www.stats.ox.ac.uk/pub/MASS4###cloud.r-project.org###focal-cran40---EOL---"
b"###r-cran-mass###r-cran-mass###r-cran-mass###r-cran-mass=7.3-55-1.2004.0###r-cran-mass###r-cran-mass###7.3-55-1.2004.0###7.3-54-1.2004.0###1115752###package###CRAN###GNU R package of Venables and Ripley's MASS###The MASS package provides functions and datasets to support the book 'Modern Applied Statistics with S' (4th edition) by W.N. Venables and B.D. Ripley. The following URL provides more details about the book: URL: http://www.stats.ox.ac.uk/pub/MASS4###cloud.r-project.org###focal-cran40---EOL---"

Yesterday I have manually updated libgdal-dev to 3.4.0 already.

clefebvre commented 2 years ago

ah ok, then it won't show up anymore no matter what.

florisvdh commented 2 years ago

I have an older system state (of several weeks ago) available on another disk (due to a hardware switch). With that I could reproduce the process (repeatedly, if adding a Timeshift snapshot), if that could help. In such case, please let me know which information to collect during that process.

Yesterday I have manually updated libgdal-dev to 3.4.0 already.

I had done exactly the same to solve same problem on a previous occasion (update from 3.2.1 to 3.3.2 IIRC), so this behaviour will probably re-occur on future occasions.

florisvdh commented 2 years ago

Here we go, after winding back:

State before updating to recent package versions from PPA

(and after updating everything else except this version of QGIS which also needs the new PPA package versions)

$ /usr/lib/linuxmint/mintUpdate/checkAPT.py
b'###qgis###qgis###qgis###qgis=1:3.22.3+32focal-ubuntugis###qgis###python3-qgis, qgis-common, libqgis-customwidgets, qgis-plugin-grass, qgis, qgis-provider-grass, qgis-providers-common, qgis-plugin-grass-common, qgis-providers, python3-qgis-common###1:3.22.3+32focal-ubuntugis###1:3.22.2+32focal-ubuntugis###64725388###package###QGIS project###Geographic Information System (GIS)###A Geographic Information System (GIS) manages, analyzes, and displays databases of geographic information. QGIS supports shape file viewing and editing, spatial data storage with PostgreSQL/PostGIS, projection on-the-fly, map composition, and a number of other features via a plugin interface. QGIS also supports display of various georeferenced raster and Digital Elevation Model (DEM) formats including GeoTIFF, Arc/Info ASCII Grid, and USGS ASCII DEM.###qgis.org###focal---EOL---'
b'###grass###grass###grass###grass=7.8.6-1~focal2###grass###grass-doc, grass-gui, grass, grass-core###7.8.6-1~focal2###7.8.6-1~focal1###44262760###package###LP-PPA-ubuntugis-ubuntugis-unstable###Geographic Resources Analysis Support System (GRASS GIS)###Commonly referred to as GRASS, this is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies.\n\nInstall this virtual package to get a full GRASS system.###ppa.launchpad.net###focal---EOL---'
b'###saga###saga###saga###saga=7.3.0+dfsg-7~focal0###saga###saga-common, libsaga-gdi-7.3.0, libsaga-api-7.3.0, saga###7.3.0+dfsg-7~focal0###7.3.0+dfsg-5~focal1###6402636###package###LP-PPA-ubuntugis-ubuntugis-unstable###System for Automated Geoscientific Analyses###SAGA GIS (System for Automated Geoscientific Analyses) is a free and open source geographic information system used for editing and analysing spatial data. It includes a large number of modules for the analysis of vector (point, line and polygon), table, grid and image data. Among others the package includes modules for geostatistics, image classification, projections, simulation of dynamic processes (hydrology, landscape development) and terrain analysis. The functionality can be accessed through a GUI, the command line or by using the C++ API.###ppa.launchpad.net###focal---EOL---'
b'###geos###geos###geos###geos=3.10.1-1~focal0###libgeos-c1v5###libgeos-c1v5, libgeos-dev, libgeos++-dev###3.10.1-1~focal0###3.9.1-1~focal0###404332###package###LP-PPA-ubuntugis-ubuntugis-unstable###Geometry engine for Geographic Information Systems - C Library###GEOS provides a spatial object model and fundamental geometric functions. It implements the geometry model defined in the OpenGIS Consortium Simple Features Specification for SQL. Functions provided include:\n\n* spatial predicates (based on the DE-9IM model), * overlay functions (intersection, difference, union, symmetric difference), * buffer, * convex hull, * area and distance functions, and * topological validity checking\n\nThis package contains the C library.###ppa.launchpad.net###focal---EOL---'
b'###pdal###pdal###pdal###pdal=2.2.0+ds-1~focal3###pdal###libpdal-plugin-e57, libpdal-util12, libpdal-plugin-i3s, libpdal-plugins, libpdal-plugin-hdf, libpdal-plugin-icebridge, libpdal-plugin-pgpointcloud, libpdal-base12, libpdal-plugin-faux, pdal###2.2.0+ds-1~focal3###2.2.0+ds-1~focal2###2958708###package###LP-PPA-ubuntugis-ubuntugis-unstable###Point Data Abstraction Library###PDAL is a BSD licensed library for translating and manipulating point cloud data of various formats. PDAL can be used to read, write and translate point cloud data in many formats. Support is included for input files of LAS, LAZ, SBET, BPF, QFIT and others. PDAL can also read from and write to databases that support point cloud storage, including Oracle, Postgres and SQLite.\n\nPDAL should not be confused with PCL (Point Cloud Library). PCL is a library specifically designed to provide algorithmic analysis and modification of point clouds. PDAL provides a limited interface to the facilities of PCL, but does not in general attempt to duplicate its capabilities.\n\nThis package contains the PDAL utilities.###ppa.launchpad.net###focal---EOL---'
b'###spatialite###spatialite###spatialite###spatialite=5.0.1-2~focal0###libsqlite3-mod-spatialite###libsqlite3-mod-spatialite, libspatialite7, libspatialite-dev###5.0.1-2~focal0###5.0.0-1~focal1###5480748###package###LP-PPA-ubuntugis-ubuntugis-unstable###Geospatial extension for SQLite - loadable module###The SpatiaLite extension enables SQLite to support spatial (geometry) data in a way conformant to OpenGis specifications, with both WKT and WKB formats.\n\nSpatialite also includes Virtualshape and Virtualtext to enable accessing shapefiles and csv/text files as virtual tables.\n\nThis package contains the loadable extension module for SQLite 3.###ppa.launchpad.net###focal---EOL---'
b'###gdal###gdal###gdal###gdal=3.4.0+dfsg-1~focal0###gdal-bin###gdal-bin, python3-gdal, gdal-data###3.4.0+dfsg-1~focal0###3.3.2+dfsg-2~focal2###2048452###package###LP-PPA-ubuntugis-ubuntugis-unstable###Geospatial Data Abstraction Library - Utility programs###GDAL is a translator library for raster geospatial data formats. As a library, it presents a single abstract data model to the calling application for all supported formats. The related OGR library (which lives within the GDAL source tree) provides a similar capability for simple features vector data.\n\nGDAL supports 40+ popular data formats, including commonly used ones (GeoTIFF, JPEG, PNG and more) as well as the ones used in GIS and remote sensing software packages (ERDAS Imagine, ESRI Arc/Info, ENVI, PCI Geomatics). Also supported many remote sensing and scientific data distribution formats such as HDF, EOS FAST, NOAA L1B, NetCDF, FITS.\n\nOGR library supports popular vector formats like ESRI Shapefile, TIGER data, S57, MapInfo File, DGN, GML and more.\n\nThis package contains utility programs, based on GDAL/OGR library, namely gdal_translate, gdalinfo, gdaladdo, gdalwarp, ogr2ogr, ogrinfo, ogrtindex.###ppa.launchpad.net###focal---EOL---'
b'###proj###proj###proj###proj=8.2.0-1~focal0###proj-bin###libproj-dev, proj-bin, proj-data###8.2.0-1~focal0###7.2.1-1~focal0###9489848###package###LP-PPA-ubuntugis-ubuntugis-unstable###Cartographic projection library (tools)###Proj and invproj perform respective forward and inverse transformation of cartographic data to or from Cartesian data with a wide range of selectable projection functions (over 100 projections).\n\nGeod and invgeod perform geodesic (Great Circle) computations for determining latitude, longitude and back azimuth of a terminus point given a initial point latitude, longitude, azimuth and distance (direct) or the forward and back azimuths and distance between an initial and terminus point latitudes and longitudes (inverse).\n\nThis package provides the PROJ binary tools.###ppa.launchpad.net###focal---EOL---'
b'###libgeotiff###libgeotiff###libgeotiff###libgeotiff=1.7.0-2~focal1###libgeotiff5###libgeotiff5, libgeotiff-dev###1.7.0-2~focal1###1.7.0-2~focal0###169592###package###LP-PPA-ubuntugis-ubuntugis-unstable###GeoTIFF (geografic enabled TIFF) library -- run-time files###This C library supports TIFF 6.0 based interchange format for georeferenced raster imagery. The GeoTIFF standard has been developed for reading, and writing geographic meta-information tags on top of TIFF raster.\n\nThis package contains the shared library only.###ppa.launchpad.net###focal---EOL---'
b'###python-pyproj###python-pyproj###python-pyproj###python-pyproj=3.2.1-2~focal0###python3-pyproj###python3-pyproj###3.2.1-2~focal0###2.6.1+ds-2~focal2###368912###package###LP-PPA-ubuntugis-ubuntugis-unstable###Python 3 interface to PROJ library###PROJ performs cartographic transformations between geographic (lat/lon) and map projection (x/y) coordinates. It can also transform directly from one map projection coordinate system to another.\n\nThis is a Python 3 binding to PROJ, it can receive coordinates as numpy arrays, Python arrays, lists or scalars. This module is optimized for numpy arrays.###ppa.launchpad.net###focal---EOL---'

image

Applying all updates in mintUpdate

image

(libpdal-dev not to be confused with libgdal-dev)

Final state

image

$ /usr/lib/linuxmint/mintUpdate/checkAPT.py
$
$ apt list --upgradable | grep gdal

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

libgdal-dev/focal 3.4.0+dfsg-1~focal0 amd64 [upgradable from: 3.3.2+dfsg-2~focal2]
$ 
$ apt policy libgdal-dev
libgdal-dev:
  Installed: 3.3.2+dfsg-2~focal2
  Candidate: 3.4.0+dfsg-1~focal0
  Version table:
     3.4.0+dfsg-1~focal0 500
        500 http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu focal/main amd64 Packages
 *** 3.3.2+dfsg-2~focal2 100
        100 /var/lib/dpkg/status
     3.0.4+dfsg-1build3 500
        500 http://mirror.unix-solutions.be/ubuntu focal/universe amd64 Packages
$
$ dpkg -l | grep libgdal-dev
ii  libgdal-dev                                   3.3.2+dfsg-2~focal2                         amd64        Geospatial Data Abstraction Library - Development files
$ 
$ dpkg --get-selections libgdal-dev
libgdal-dev                 install

So checkAPT.py returns nothing, consistent with the GUI.

florisvdh commented 2 years ago

Another bunch of updates is available from this PPA. The same as above is going to happen, i.e. libgdal-dev will not be picked up by mintUpdate, contrary to the apt tools:

$ /usr/lib/linuxmint/mintUpdate/checkAPT.py
b'###grass###grass###grass###grass=8.0.2-1~focal0###grass###grass-doc, grass-gui, grass, grass-core###8.0.2-1~focal0###7.8.6-1~focal2###42842388###package###LP-PPA-ubuntugis-ubuntugis-unstable###Geographic Resources Analysis Support System (GRASS GIS)###Commonly referred to as GRASS, this is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies.\n\nInstall this virtual package to get a full GRASS system.###ppa.launchpad.net###focal---EOL---'
b'###gdal###gdal###gdal###gdal=3.4.3+dfsg-1~focal0###gdal-bin###libgdal30, gdal-bin, python3-gdal, gdal-data###3.4.3+dfsg-1~focal0###3.4.0+dfsg-1~focal0###9429320###package###LP-PPA-ubuntugis-ubuntugis-unstable###Geospatial Data Abstraction Library - Utility programs###GDAL is a translator library for raster geospatial data formats. As a library, it presents a single abstract data model to the calling application for all supported formats. The related OGR library (which lives within the GDAL source tree) provides a similar capability for simple features vector data.\n\nGDAL supports 40+ popular data formats, including commonly used ones (GeoTIFF, JPEG, PNG and more) as well as the ones used in GIS and remote sensing software packages (ERDAS Imagine, ESRI Arc/Info, ENVI, PCI Geomatics). Also supported many remote sensing and scientific data distribution formats such as HDF, EOS FAST, NOAA L1B, NetCDF, FITS.\n\nOGR library supports popular vector formats like ESRI Shapefile, TIGER data, S57, MapInfo File, DGN, GML and more.\n\nThis package contains utility programs, based on GDAL/OGR library, namely gdal_translate, gdalinfo, gdaladdo, gdalwarp, ogr2ogr, ogrinfo, ogrtindex.###ppa.launchpad.net###focal---EOL---'
b'###geos###geos###geos###geos=3.10.2-1~focal0###libgeos-c1v5###libgeos-c1v5, libgeos-dev, libgeos++-dev###3.10.2-1~focal0###3.10.1-1~focal0###520100###package###LP-PPA-ubuntugis-ubuntugis-unstable###Geometry engine for Geographic Information Systems - C Library###GEOS provides a spatial object model and fundamental geometric functions. It implements the geometry model defined in the OpenGIS Consortium Simple Features Specification for SQL. Functions provided include:\n\n* spatial predicates (based on the DE-9IM model), * overlay functions (intersection, difference, union, symmetric difference), * buffer, * convex hull, * area and distance functions, and * topological validity checking\n\nThis package contains the C library.###ppa.launchpad.net###focal---EOL---'
b'###libgeotiff###libgeotiff###libgeotiff###libgeotiff=1.7.1-1~focal0###libgeotiff5###libgeotiff5, libgeotiff-dev###1.7.1-1~focal0###1.7.0-2~focal1###170940###package###LP-PPA-ubuntugis-ubuntugis-unstable###GeoTIFF (geografic enabled TIFF) library -- run-time files###This C library supports TIFF 6.0 based interchange format for georeferenced raster imagery. The GeoTIFF standard has been developed for reading, and writing geographic meta-information tags on top of TIFF raster.\n\nThis package contains the shared library only.###ppa.launchpad.net###focal---EOL---'
$ 
$ apt list --upgradable | grep gdal

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

gdal-bin/focal 3.4.3+dfsg-1~focal0 amd64 [upgradable from: 3.4.0+dfsg-1~focal0]
gdal-data/focal,focal 3.4.3+dfsg-1~focal0 all [upgradable from: 3.4.0+dfsg-1~focal0]
libgdal-dev/focal 3.4.3+dfsg-1~focal0 amd64 [upgradable from: 3.4.0+dfsg-1~focal0]
libgdal30/focal 3.4.3+dfsg-1~focal0 amd64 [upgradable from: 3.4.0+dfsg-1~focal0]
python3-gdal/focal 3.4.3+dfsg-1~focal0 amd64 [upgradable from: 3.4.0+dfsg-1~focal0]
$ 
$ dpkg -l | grep libgdal-dev
ii  libgdal-dev                                   3.4.0+dfsg-1~focal0                         amd64        Geospatial Data Abstraction Library - Development files
$ 
$ apt policy libgdal-dev
libgdal-dev:
  Installed: 3.4.0+dfsg-1~focal0
  Candidate: 3.4.3+dfsg-1~focal0
  Version table:
     3.4.3+dfsg-1~focal0 500
        500 http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu focal/main amd64 Packages
 *** 3.4.0+dfsg-1~focal0 100
        100 /var/lib/dpkg/status
     3.0.4+dfsg-1build3 500
        500 http://mirror.unix-solutions.be/ubuntu focal/universe amd64 Packages

I have not yet applied these updates.

florisvdh commented 2 years ago

This is with mintUpdate 5.7.8 on Linux Mint 20 Cinnamon.

florisvdh commented 2 years ago

@clefebvre if you'd like me to investigate something before applying the upgrade of these packages, please let me know. Planning to do this upgrade in a few days.

florisvdh commented 1 year ago

The described problem did not pop up with the latest libgdal-dev update (several months ago) in Linux Mint 20, nor did it (yesterday) in Linux Mint 21.

So closing this issue.