cannot restore from snapshot

[achubaty]

See the following examples:

• https://github.com/PredictiveEcology/WBI_forecasts/blob/development/packageVersions_clean.txt
• https://github.com/PredictiveEcology/WBI_forecasts/blob/development/packageVersionsAMC.txt
• https://github.com/PredictiveEcology/LandWeb/blob/rework-config/packages_2022-03-22.txt
• https://github.com/FOR-CAST/Ontario_AOU_ROF/blob/development/packageVersions_2023-03-21.txt

There are several points of failure, including using the branch name instead of the SHA to restore GitHub packages. Branches may have been deleted (so it will fail outright), or may have been updated since the snapshot (so instead of getting the commit requested, it's installing the latest from that branch).

[eliotmcintire]

What is the expected behaviour in these cases, when there is a conflict between branch and SHA?

[achubaty]

It should always use the SHA, never the branch name, to install the specific version of the package in the snapshot.

[eliotmcintire]

Are you able to provide the actual error/fail and how you detect that there was a problem in one of those examples?

[achubaty]

tmplib <- file.path(tempdir(), "reprexlib")
dir.create(tmplib)
.libPaths(tmplib, include.site = FALSE)
.libPaths()

## NOTE: needs R 4.1 !!
snpsht <- tempfile("packageVersions_", fileext = ".txt")
download.file("https://raw.githubusercontent.com/PredictiveEcology/WBI_forecasts/development/packageVersions_clean.txt", snpsht)

install.packages(c("Require", "remotes"))
library(Require)

tmpcache <- file.path(tempdir(), "reprexcache")
dir.create(tmpcache)
options(Require.RPackageCache = tmpcache)

Require(packageVersionFile = snpsht)

Getting dependencies for 307 packages on CRAN; 16 packages on GitHub
available.packages() does not have correct information on package dependencies for BH (==1.78.0-0); checking CRAN archives
available.packages() does not have correct information on package dependencies for DBI (==1.1.2); checking CRAN archives
available.packages() does not have correct information on package dependencies for DEoptim (==2.2-6); checking CRAN archives
available.packages() does not have correct information on package dependencies for DEoptimR (==1.0-10); checking CRAN archives
available.packages() does not have correct information on package dependencies for EnvStats (==2.5.0); checking CRAN archives
Using GITHUB_PAT to access files on GitHub
available.packages() does not have correct information on package dependencies for MatrixModels (==0.5-0); checking CRAN archives
available.packages() does not have correct information on package dependencies for MuMIn; checking CRAN archives
available.packages() does not have correct information on package dependencies for R.methodsS3 (==1.8.1); checking CRAN archives
available.packages() does not have correct information on package dependencies for R.oo (==1.24.0); checking CRAN archives
available.packages() does not have correct information on package dependencies for R.utils (==2.11.0); checking CRAN archives
available.packages() does not have correct information on package dependencies for RApiSerialize (==0.1.0); checking CRAN archives
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available.packages() does not have correct information on package dependencies for gamlss.dist (==6.0-1); checking CRAN archives
available.packages() does not have correct information on package dependencies for gargle (==1.2.0); checking CRAN archives
available.packages() does not have correct information on package dependencies for gbm (==2.1.8); checking CRAN archives
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available.packages() does not have correct information on package dependencies for spdep (==1.2-2); checking CRAN archives
available.packages() does not have correct information on package dependencies for stringfish (==0.15.5); checking CRAN archives
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available.packages() does not have correct information on package dependencies for terra (==1.5-21); checking CRAN archives
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available.packages() does not have correct information on package dependencies for tibble (==3.1.6); checking CRAN archives
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available.packages() does not have correct information on package dependencies for viridisLite (==0.4.0); checking CRAN archives
available.packages() does not have correct information on package dependencies for waldo (==0.3.1); checking CRAN archives
available.packages() does not have correct information on package dependencies for whisker (==0.4); checking CRAN archives
available.packages() does not have correct information on package dependencies for withr (==2.4.3); checking CRAN archives
available.packages() does not have correct information on package dependencies for wk (==0.6.0); checking CRAN archives
available.packages() does not have correct information on package dependencies for xfun (==0.29); checking CRAN archives
available.packages() does not have correct information on package dependencies for yaml (==2.2.2); checking CRAN archives
available.packages() does not have correct information on package dependencies for yulab.utils (==0.0.4); checking CRAN archives
available.packages() does not have correct information on package dependencies for zip (==2.2.0); checking CRAN archives
available.packages() does not have correct information on package dependencies for zoo (==1.8-9); checking CRAN archives
... 232 of these have recursive dependencies           
           
  1 of 232
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available.packages() does not have correct information on package dependencies for MuMIn (>= 1.42.5); checking CRAN archives
MuMIn (>= 1.42.5) dependencies not found on CRAN; perhaps incomplete description? On GitHub?
  6 of 232
LandR dependencies not found on CRAN; perhaps incomplete description? On GitHub?
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available.packages() does not have correct information on package dependencies for SpaDES.core; checking CRAN archives
 23 of 232
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Error in getSHAfromGitHub(...) : 
  Can't find terraInProjectInputs on GitHub repo PredictiveEcology/reproducible; 
 -- does it exist? --

[achubaty]

missing branch case is easy to spot ^^

In other cases, I see it downloading and attempting to install from HEAD instead of using specific SHA, or there are other flat out errors.

[eliotmcintire]

Working through these... there are issues that I do not know if they can be addressed.

The error that is posted (terraInProjectInputs) is listed as a Remotes within the package climateData...

> readLines(a$DESCFile)
 [1] "Package: climateData"                                                                 
 [2] "Title: Utilities For Working With North American Climate Data"                        
 [3] "Description: Utilities for working with North American climate data from"             
 [4] "    'ClimateNA' <http://climatena.ca/>."                                              
 [5] "URL: https://github.com/PredictiveEcology/climateData"                                
 [6] "Date: 2022-01-27"                                                                     
 [7] "Version: 0.0.0.9005"                                                                  
 [8] "Authors@R: c("                                                                        
 [9] "    person(\"Alex M\", \"Chubaty\", email = \"achubaty@for-cast.ca\","                
[10] "           role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7146-8135\")),"
[11] "    person(\"Ian\", \"Eddy\", email = \"ian.eddy@nrcan-rncan.gc.ca\","                
[12] "           role = c(\"aut\"), comment = c(ORCID = \"0000-0001-7397-2116\")),"         
[13] "    person(\"Eliot\", \"McIntire\", email = \"eliot.mcintire@nrcan-rncan.gc.ca\","    
[14] "           role = c(\"aut\"), comment = c(ORCID = \"0000-0002-6914-8316\"))"          
[15] "    )"                                                                                
[16] "Depends:"                                                                             
[17] "    R (>= 3.6)"                                                                       
[18] "Imports:"                                                                             
[19] "    data.table,"                                                                      
[20] "    magrittr,"                                                                        
[21] "    raster,"                                                                          
[22] "    reproducible (>= 1.2.8.9014),"                                                    
[23] "    sp,"                                                                              
[24] "    stats,"                                                                           
[25] "    utils"                                                                            
[26] "Remotes:"                                                                             
[27] "    PredictiveEcology/reproducible@terraInProjectInputs"                              
[28] "BugReports: https://github.com/PredictiveEcology/climateData/issues"                  
[29] "Encoding: UTF-8"                                                                      
[30] "Language: en-CA"                                                                      
[31] "License: GPL-3"                                                                       
[32] "ByteCompile: yes"                                                                     
[33] "LazyData: true"                                                                       
[34] "RoxygenNote: 7.1.2"                                                                   
[35] "Suggests: "                                                                           
[36] "    knitr,"                                                                           
[37] "    rmarkdown"                                                                        
[38] "VignetteBuilder: knitr"  

There is nothing in this that specifies a SHA for the package reproducible that is the one failing -- and it is not failing during "install"... but during the assessment of the recursive package dependencies of climateData, which it can't do. Where would Require be able to find the SHA that was installed. In this case, the packageSnapshot.txt file does have a listing for reproducible that is NOT the one that would have been installed from that feature branch (terraInProjectInputs) because it has no SHA associated with it in the file. So, in this case, is the correct behaviour to "not fail" when it is looking for the recursive dependencies of climateData when one of the dependencies doesn't exist? I think the only way this would be "ok" behaviour is because the call to pkgDep is inside a call to Require where all dependencies are supposed to be described (which they aren't).

I will look at the other 4 examples, but my hunch is they are related fails...

[eliotmcintire]

I have made this scenario not fail, but give a warning. Essentially, one package that is specified with a SHA has a dependency on GitHub that is specified in the Remotes section of the DESCRIPTION file. Now if that branch does not exist, it will revert to the main branch to evaluate the required dependencies, with a warning.

I have not made it through the other 3 examples.

It does seem, however, that these and all other examples of "failing" snapshots is due to the organic nature of installations in the first place ... that allow for violations to occur incrementally, but then taking a snapshot will create version violations that are illegal. Thus, restoring from those requires a series of rules that allow for (accommodate by changing the requested package versions) these violations.

[eliotmcintire]

@achubaty can you please test these again with new Require 1.0.0

[achubaty]

first WBI example fails using latest Require (v1.0.1)

Error in getDepsGH(pkgDTCached[["FALSE"]][isGH], verbose, which = which,  : 
  Error in getSHAfromGitHub(...) : 
  Can't find PredictiveEcology/reproducible@terraInProjectInputs; 
 -- does it exist? --
In addition: Warning messages:
1: partial match of 'installed' to 'installedSha' 
2: partial match of 'installed' to 'installedSha'