ainstall

[MarcinKosinski]

for a specific md5hash, asession gives packages and versions under which it was created, maybe one should create ainstall function that install specific versions of R packages with the usage of this package https://cran.r-project.org/web/packages/versions/index.html

[pbiecek]

Cool idea, but I am not sure if it's possible for github packages or own
packages installed from source (tag.gz files).

2016-02-17 16:06 GMT+01:00 Marcin Kosiński notifications@github.com:

for a specific md5hash, asession gives packages and versions under which
it was created, maybe one should create ainstall function that install
specific versions of R packages with the usage of this package
https://cran.r-project.org/web/packages/versions/index.html

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#251.

pozdrawiam serdecznie,
Przemysław Biecek

[MarcinKosinski]

Or we can add a note to asession documentation about this feature.

[MarcinKosinski]

'versions' fits in the narrow gap between the 'devtools' install_version() function and the 'checkpoint' package. devtools::install_version() installs a stated package version from source files stored on the CRAN archives. However CRAN does not store binary versions of packages so Windows users need to have RTools installed and Windows and OSX users get longer installation times. 'checkpoint' uses the Revolution Analytics MRAN server to install packages (from source or binary) as they were available on a given date.

[MarcinKosinski]

#255

[MarcinKosinski]

I went with devtools::install_version (but it does not support lib parameter passed to install.packages, so I also neededtouse .libPaths() :

check this out

# Recreate packages library for artifact
Marcin Kosiński  
27 lutego 2016  



# Retrieve object created with archive-version of ggplot2


```r
library(devtools)
install.packages('ggplot2', repos = 'https://cran.rstudio.com/')
library(ggplot2)
devtools::session_info(pkgs = 'ggplot2')

adir <- 'adir'
dir.create(adir)
.libPaths(c(adir, .libPaths())) # lib argument in devtools does not work
install.packages('devtools', repos = 'https://cran.rstudio.com/')
devtools::install_version('ggplot2', version = '1.0.1', lib = adir, repos = 'https://cran.rstudio.com/')
library(ggplot2, lib = adir)
devtools::session_info('ggplot2')

arecreate()

library(archivist)
system.file('graphGallery', package = 'archivist') -> archivist.dir
setLocalRepo(archivist.dir)
arecreate.dir <- 'arecreate.dir' 
dir.create('arecreate.dir')

arecreate <- function(md5hash = '600bda83cb840947976bd1ce3a11879d', lib, repos = 'https://cran.rstudio.com/' ){

  old_lib <- .libPaths()
  new_lib <- .libPaths(lib)

  # probably local installations or GitHub packages
  NOT_CRAN <- which(asession(md5hash)$packages[, '*'] == '*')

  CRAN_PKGS <- grep('CRAN',
                    x = asession(md5hash)$packages[, 'source'])
  GITHUB_PKGS <- grep('Github',
                    x = asession(md5hash)$packages[, 'source'])
  # reinstall CRAN packages

  sapply(setdiff(CRAN_PKGS, NOT_CRAN), function(package){
    devtools::install_version(asession(md5hash)$packages[package, 'package'],
                                 version = asession(md5hash)$packages[package, 'version'], 
                                 lib = lib, repos = repos )
  })
  # extract commits and names from parenthesis
  gsub("[\\(\\)]",
       "", 
       regmatches(asession(md5hash)$packages[GITHUB_PKGS, 'source'],
                  gregexpr("\\(.*?\\)",
                           asession(md5hash)$packages[GITHUB_PKGS, 'source'])
                  )[[1]]
       ) -> GITHUB_NAMES
    # reinstall GitHub packages
  devtools::install_github(GITHUB_NAMES, lib = lib)
  .libPaths(old_lib)
}
arecreate('600bda83cb840947976bd1ce3a11879d', lib = arecreate.dir)

knitr::kable(installed.packages(arecreate.dir))

[pbiecek]

There is a lot of calls to asession(md5hash)
You can call this function just one time, and then use the results.

But larger problem is that it is not working on OSX ;-)

tar: Unrecognized archive format
tar: Error exit delayed from previous errors.
Error: file ‘/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T//RtmpUP1PxN/downloaded_packages/assertthat_0.1.tgz’ is not an OS X binary package
In addition: Warning message:
'tar' returned non-zero exit code 1 

You need to add , type="source" to the install_version() function.

I will do more tests in a few days

[pbiecek]

I was thinking about other possible names fir this function.
Maybe something that is relates with revert or restore`
(since it reverts/restores previous versions of packages)?

[MarcinKosinski]

libraryRestore? arestore?
So if it does not work for MAC OSX, so we'd better move to versions
package when this goldingn/versions#7 will be
fixed

2016-02-28 23:47 GMT+01:00 Przemysław Biecek notifications@github.com:

I was thinking about other possible names fir this function.
Maybe something that is relates with revert or restore`
(since it reverts/restores previous versions of packages)?

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[pbiecek]

It will work,
you just need to add type="source" to the install_version()

I like libraryRestore more, since the name is more self explanatory,
or maybe restoreLibrary / revertLibrary, since in other functions the verb is first.

[pbiecek]

I've added restoreLibs() function. There are some dirty solutions, so I will think more about alternatives. But at least it is working for ggplot2 objects

[MarcinKosinski]

I've added devtools check - if it is installed - since we do not have imports from devtools 400216c

[MarcinKosinski]

By now restoreLibs downgrades artifacts in the first library of .libPaths() . Wouldn't it be a good idea to install old packages in a new directory, that would not change the state of packages used by user on a daily routine? I think additional parameter lib.loc could solve such demand or we could add additional information to manual page, that a user could manually change .libPaths() on his own.

If that's ok for you additional example to restoreLibs could look something like this

  old_lib <- .libPaths()
  new_lib <- .libPaths(new_directory)
  restoreLibs()
 .libPaths(old_lib)

[pbiecek]

It will be a good solution and I saw it in your proposition
but this was not working,
the .libPaths was not changing library to a specified folder
(al least not on OSX)

2016-03-05 18:37 GMT+01:00 Marcin Kosiński notifications@github.com:

By now restoreLibs downgrades artifacts in the first library of
.libPaths() . Wouldn't it be a good idea to install old packages in a new
directory, that would not change the state of packages used by user on a
daily routine? I think additional parameter lib.loc could solve such
demand or we could add additional information to manual page, that a user
could manually change .libPaths() on his own.

If that's ok for you additional example to restoreLibs could look
something like this

old_lib <- .libPaths()
new_lib <- .libPaths(lib)
restoreLibs()
.libPaths(old_lib)

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#251 (comment).

pozdrawiam serdecznie,
Przemysław Biecek

[MarcinKosinski]

Could you provide a reproducible example of that situation on OSX?
Something like codes and results of

.libPaths() -> x
x
.libPaths(tempfile()) -> y
y
.libPaths(x)

I'll post that case on StackOverflow

2016-03-05 20:07 GMT+01:00 Przemysław Biecek notifications@github.com:

It will be a good solution and I saw it in your proposition
but this was not working,
the .libPaths was not changing library to a specified folder
(al least not on OSX)

2016-03-05 18:37 GMT+01:00 Marcin Kosiński notifications@github.com:

By now restoreLibs downgrades artifacts in the first library of
.libPaths() . Wouldn't it be a good idea to install old packages in a new
directory, that would not change the state of packages used by user on a
daily routine? I think additional parameter lib.loc could solve such
demand or we could add additional information to manual page, that a user
could manually change .libPaths() on his own.

If that's ok for you additional example to restoreLibs could look
something like this

old_lib <- .libPaths()
new_lib <- .libPaths(lib)
restoreLibs()
.libPaths(old_lib)

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<#251 (comment)
.

pozdrawiam serdecznie,
Przemysław Biecek

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#251 (comment).

[pbiecek]

Here it is

> (x <- .libPaths())
[1] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"
> (y <- tempfile())
[1] "/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T//Rtmp4qW3nJ/filee0df790601a4"
> (z <- .libPaths(y)) 
[1] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"

[pbiecek]

Ok, but now I see where is the problem
Argument of .libPaths() must be a directory
this one will work.

> (y <- tempfile())
[1] "/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T//Rtmp4qW3nJ/filee0df3fc1811d"
> dir.create(y)
> (z <- .libPaths(y)) 
[1] "/private/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T/Rtmp4qW3nJ/filee0df3fc1811d"
[2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"                      
> .libPaths()
[1] "/private/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T/Rtmp4qW3nJ/filee0df3fc1811d"
[2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library" 

[MarcinKosinski]

Yes, that's the case. But I still have problems here
#255 (comment)

2016-03-05 21:00 GMT+01:00 Przemysław Biecek notifications@github.com:

Ok, but now I see where is the problem
Argument of .libPaths() must be a directory
this one will work.

(y <- tempfile())
[1] "/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T//Rtmp4qW3nJ/filee0df3fc1811d"
dir.create(y)
(z <- .libPaths(y))
[1] "/private/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T/Rtmp4qW3nJ/filee0df3fc1811d"
[2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"
.libPaths()
[1] "/private/var/folders/_l/jllqh32s3llbxmtrh2431vpr0000gn/T/Rtmp4qW3nJ/filee0df3fc1811d"
[2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"

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