Rebuild binaries when a LinkingTo dependency changes

On 26/09/2023, at 12:28 PM, Kirill M?ller <kirill at cynkra.com> wrote:

Thanks, Simon and Uwe, for your inputs.

It's not that TMB requires a particular version of Matrix, it just suggests using the same version of Matrix as it was built with. We may have seen this problem before, with innocuous changes in Rcpp breaking downstream packages.

A different example, running in two separate sessions for comparison, is shown below.

Windows may be rebuilding more often than strictly necessary, but it seems the right thing to do to me. We could assess the overhead using historic data to see how big of an impact that would be.

I hear you're proposing that the TMB maintainers release an updated version whenever Matrix is updated?

Best regards

Kirill



# Example 1: happy path

dir.create("templib")
.libPaths(normalizePath("templib"))
Sys.setenv(R_LIBS_USER = .libPaths()[[1]])

# Sanity check
rownames(installed.packages())
#>  [1] "base"       "boot"       "class"      "cluster"    "codetools" 
#>  [6] "compiler"   "datasets"   "foreign"    "graphics"   "grDevices" 
#> [11] "grid"       "KernSmooth" "lattice"    "MASS"       "Matrix"    
#> [16] "methods"    "mgcv"       "nlme"       "nnet"       "parallel"  
#> [21] "rpart"      "spatial"    "splines"    "stats"      "stats4"    
#> [26] "survival"   "tcltk"      "tools"      "utils"
packageVersion("Matrix")
#> [1] '1.5.4.1'

# Install TMB from source, now matching the Matrix version
install.packages(c("Rcpp", "RcppEigen"))
#> Installing packages into '/private/var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T/RtmpSL7Etm/reprex-bc8b35150024-vague-bull/templib'
#> (as 'lib' is unspecified)
#> 
#> The downloaded binary packages are in
#>  /var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T//RtmpOpHc0P/downloaded_packages
install.packages("TMB", type = "source", repos = "https://cloud.r-project.org/")
#> Installing package into '/private/var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T/RtmpSL7Etm/reprex-bc8b35150024-vague-bull/templib'
#> (as 'lib' is unspecified)

# Perform implicit consistency check
packageVersion("Matrix")
#> [1] '1.5.4.1'
requireNamespace("TMB")
#> Loading required namespace: TMB



# Example 2: upgrading Matrix after installing TMB

dir.create("templib")
.libPaths(normalizePath("templib"))
Sys.setenv(R_LIBS_USER = .libPaths()[[1]])

# Sanity check
rownames(installed.packages())
#>  [1] "base"       "boot"       "class"      "cluster"    "codetools" 
#>  [6] "compiler"   "datasets"   "foreign"    "graphics"   "grDevices" 
#> [11] "grid"       "KernSmooth" "lattice"    "MASS"       "Matrix"    
#> [16] "methods"    "mgcv"       "nlme"       "nnet"       "parallel"  
#> [21] "rpart"      "spatial"    "splines"    "stats"      "stats4"    
#> [26] "survival"   "tcltk"      "tools"      "utils"
packageVersion("Matrix")
#> [1] '1.5.4.1'

# Install TMB from source, now matching the Matrix version
install.packages(c("Rcpp", "RcppEigen"))
#> Installing packages into '/private/var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T/RtmpSL7Etm/reprex-bc8b4fff25a6-next-esok/templib'
#> (as 'lib' is unspecified)
#> 
#> The downloaded binary packages are in
#>  /var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T//RtmpyN9yHv/downloaded_packages
install.packages("TMB", type = "source", repos = "https://cloud.r-project.org/")
#> Installing package into '/private/var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T/RtmpSL7Etm/reprex-bc8b4fff25a6-next-esok/templib'
#> (as 'lib' is unspecified)

# Upgrading Matrix
install.packages("Matrix")
#> Installing package into '/private/var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T/RtmpSL7Etm/reprex-bc8b4fff25a6-next-esok/templib'
#> (as 'lib' is unspecified)
#> 
#> The downloaded binary packages are in
#>  /var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T//RtmpyN9yHv/downloaded_packages

# Perform implicit consistency check
packageVersion("Matrix")
#> [1] '1.6.1.1'
requireNamespace("TMB")
#> Loading required namespace: TMB
#> Warning in checkMatrixPackageVersion(): Package version inconsistency detected.
#> TMB was built with Matrix version 1.5.4.1
#> Current Matrix version is 1.6.1.1
#> Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package



On 25.09.23 15:22, Simon Urbanek wrote:

Kirill,

we have no way of knowing when a packages introduced a breaking change (which it really shouldn't), so the maintainers would have to inform as (Matrix authors did inform us that 1.6.0 introduces breaking change so that's why we did a manual re-bulid on that update). Also checking exact version (like TMB seems to do) doesn't work for the same reason and is not a good way to deal with the problem - we cannot re-build all packages with each change, because of the amount of time that would take (by now it takes more that a day to re-build CRAN just for one R target) and more fundamental problem with re-builds:

The real problem here is deeper than just triggering rebuilds: the users have no way of knowing if a package has been re-built and updated, because the version does not change. If let's say TMB is release 1.0 used Matrix 1.6.0 and then Matrix is updated to 1.6.1 then TMB cannot require it because it did not bump its version, i.e. the binary for TMB 1.0 with Matrix 1.6.0 is indistinguishable from a binary of TMB 1.0 with Matrix 1.6.1 on CRAN so if the user used update.packages() it would not count as a new TMB version. Therefore TMB really has to update its version from 1.0 to let's say 1.0-1 if it requests a rebuild against changes in Matrix 1.6.1. Clearly, this is not ideal, but currently there is other way that would guarantee consistency of binaries. We are aware of the problem and we are we are in fact thinking about possible solutions (special tags on binary versions) for future version of R, but for now the package authors have to be aware of potential breakage upstream.

Cheers,
Simon

On 26/09/2023, at 7:46 AM, Kirill M?ller via R-SIG-Mac <r-sig-mac at r-project.org>
 wrote:

Hi


The TMB package has Matrix in its LinkingTo dependencies. In a clean package library, I see behavior posted below.

Should the TMB package have been rebuilt when a new version of the Matrix package was pushed? More general, should we rebuild all reverse LinkingTo dependencies of a package that gets an update on CRAN? This will mean a lot of package rebuilds with Rcpp, but also a lot less frustration down the road. Thanks!


Best regards

Kirill


dir.create("templib")
.libPaths(normalizePath("templib"))

# Sanity check
rownames(installed.packages())
#>  [1] "base"       "boot"       "class"      "cluster" "codetools"
#>  [6] "compiler"   "datasets"   "foreign"    "graphics" "grDevices"
#> [11] "grid"       "KernSmooth" "lattice"    "MASS" "Matrix"
#> [16] "methods"    "mgcv"       "nlme"       "nnet" "parallel"
#> [21] "rpart"      "spatial"    "splines"    "stats" "stats4"
#> [26] "survival"   "tcltk"      "tools"      "utils"
packageVersion("Matrix")
#> [1] '1.5.4.1'

# Install fresh binary packages
install.packages(c("Matrix", "TMB"))
#> Installing packages into '/private/var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T/RtmpXIjIPy/reprex-87aa25cc1fa4-sugar-cob/templib'
#> (as 'lib' is unspecified)
#> also installing the dependencies 'Rcpp', 'RcppEigen'
#>
#> The downloaded binary packages are in
#> /var/folders/dj/yhk9rkx97wn_ykqtnmk18xvc0000gn/T//Rtmp4GSL7m/downloaded_packages
packageVersion("Matrix")
#> [1] '1.6.1.1'

# Perform implicit consistency check
requireNamespace("TMB")
#> Loading required namespace: TMB
#> Warning in checkMatrixPackageVersion(): Package version inconsistency detected.
#> TMB was built with Matrix version 1.6.0
#> Current Matrix version is 1.6.1.1
#> Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package