Install failure of R pacakge due to local paths

[s-andrews]

> install_github("StevenWingett/LifeSciencesTrainingDatasets/Trainingdata")
WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from https://cran.r-project.org/bin/windows/Rtools/.
Downloading GitHub repo StevenWingett/LifeSciencesTrainingDatasets@master
WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from https://cran.r-project.org/bin/windows/Rtools/.
√  checking for file 'C:\Users\andrewss\AppData\Local\Temp\RtmpYVV8Wb\remotes2710a79739f\StevenWingett-LifeSciencesTrainingDatasets-2b9d343\Trainingdata/DESCRIPTION' (792ms)
-  preparing 'Trainingdata':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Biochemical_Oxygen_Demand.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Biomass_of_Herbivorous_Fish.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Bird_Sighting_Texas_2018.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Brain_Bodyweight.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Child_Variants.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Childrens_Indoor_Hobbies_During_Lockdown.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Childrens_Outdoor_Hobbies_During_Lockdown.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Cuttlefish_Buoyancy.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Modern_Pollen_Plant_Diversity_Relationships.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects: 'Trainingdata/data/Neutrophils.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Plant_CO2_Uptake.rds'  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Sleep_Deprivation_CSD.rds'
-  building 'Trainingdata_0.1.0.tar.gz'

Installing package into ‘C:/Users/andrewss/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'Trainingdata' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning in gzfile(file, "rb") :
  cannot open compressed file 'D:/Documents/R/Trainingdata/data/Biochemical_Oxygen_Demand.rds', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Error: unable to load R code in package 'Trainingdata'
Execution halted
ERROR: lazy loading failed for package 'Trainingdata'
* removing 'C:/Users/andrewss/Documents/R/win-library/4.0/Trainingdata'
Error: Failed to install 'Trainingdata' from GitHub:
  (converted from warning) installation of package ‘C:/Users/andrewss/AppData/Local/Temp/RtmpYVV8Wb/file271048247ad8/Trainingdata_0.1.0.tar.gz’ had non-zero exit status

[Casey-Brown]

Should be fixed now, removed local dependencies and made a change to .rda from .rds files

[s-andrews]

Yes, it now installs successfully. I just get a bunch of warnings about:

WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'Trainingdata/data/Biochemical_Oxygen_Demand.rda'

...lots of times. Looks like you need to add an R version dependency to your config file.

[Casey-Brown]

Yeah I got those too, I was just confused as to why it had a dependency on an older version of r?

Sent from my iPhone

On 21 Jul 2020, at 11:39 am, Simon Andrews notifications@github.com wrote:



Yes, it now installs successfully. I just get a bunch of warnings about:

WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'Trainingdata/data/Biochemical_Oxygen_Demand.rda'

...lots of times. Looks like you need to add an R version dependency to your config file.

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[Casey-Brown]

Updated dependency to a more recent r version

[s-andrews]

Yeah I got those too, I was just confused as to why it had a dependency on an older version of r?

It doesn't, it has a dependency on R>=3.5, it's preventing R versions older than 3.5 using it as they don't support that RDA/S format.