Add an option to do recursive dependency search when `packrat::snapsh…

[Valdimus]

Hello,

I'm using packrat.lock to restore my packrat, but since ac1a18c, when packrat::snapshot() is invoked no more 'Require' field is add to packrat.lock file. It would be great to add an option to let the user choose if I want to enable/disable recursive dependency search.

[kevinushey]

Sorry for taking so long to respond here!

You should still see the 'Requires:' field populated even with the current GitHub master version of packrat; I just tested with a project containing the file deps.R:

library(rmarkdown)
library(data.table)

and attempting to snapshot this gave me fields like e.g.

Package: knitr
Source: CRAN
Version: 1.15.1
Requires: digest, evaluate, highr, markdown, stringr, yaml

Perhaps I'm misunderstanding something or the issue is more subtle?

[Valdimus]

Hi, I don't explain my use case correctly, sorry. I don't have any R script that load package that are installed in packrat. I use packrat for managing R packages at system level (see #357 for more information). So I have a R script that build a packrat from packrat.lock file. The problem is when I generate a packrat.lock file when a user ask me to create a new packrat from a list of desired packages or add packages to an existing one.

As example, if I have to create a packrat with bit64 in it I will do:

> library("packrat")

> # Create the packrat
> packrat::init()
Initializing packrat project in directory:
- "~/test"

Adding these packages to packrat:
            _         
    packrat   0.4.8-15

Fetching sources for packrat (0.4.8-15) ... OK (local current)
Snapshot written to '/home/christophe/test/packrat/packrat.lock'
Installing packrat (0.4.8-15) ... 
	OK (built source)
Initialization complete!
Packrat mode on. Using library in directory:
- "~/test/packrat/lib"

> # Install packages
> install.packages("bit64")
Installing package into ‘/home/christophe/test/packrat/lib/x86_64-pc-linux-gnu/3.2.3’
(as ‘lib’ is unspecified)
also installing the dependency ‘bit’

trying URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/bit_1.1-12.tar.gz'
Content type 'application/x-gzip' length 53737 bytes (52 KB)
==================================================
downloaded 52 KB

trying URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/bit64_0.9-5.tar.gz'
Content type 'application/x-gzip' length 121087 bytes (118 KB)
==================================================
downloaded 118 KB

* installing *source* package ‘bit’ ...
** package ‘bit’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c attrutil.c -o attrutil.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bit.c -o bit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chunkutil.c -o chunkutil.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c clone.c -o clone.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rle.c -o rle.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o bit.so attrutil.o bit.o chunkutil.o clone.o rle.o -L/usr/lib/R/lib -lR
installing to /home/christophe/test/packrat/lib/x86_64-pc-linux-gnu/3.2.3/bit/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (bit)
* installing *source* package ‘bit64’ ...
** package ‘bit64’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bsearch.c -o bsearch.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cache.c -o cache.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hash64.c -o hash64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c integer64.c -o integer64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sort64.c -o sort64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sortuse64.c -o sortuse64.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o bit64.so bsearch.o cache.o hash64.o integer64.o sort64.o sortuse64.o -L/usr/lib/R/lib -lR
installing to /home/christophe/test/packrat/lib/x86_64-pc-linux-gnu/3.2.3/bit64/libs
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (bit64)

The downloaded source packages are in
	‘/tmp/Rtmpgh4cU2/downloaded_packages’


> # Do a snapshot
> packrat::snapshot()

I obtain the corresponding packrat.lock file:

PackratFormat: 1.4
PackratVersion: 0.4.8.15
RVersion: 3.2.3
Repos: local=file:///home/christophe/repo/,
    CRAN=https://pbil.univ-lyon1.fr/CRAN

Package: bit
Source: CRAN
Version: 1.1-12
Hash: a4cdb11cf9fd6dd38f9f40c413b81e93

Package: bit64
Source: CRAN
Version: 0.9-5
Hash: efc07a32b683ff0c778c2c6868bfb655

Package: packrat
Source: local
Version: 0.4.8-15
Hash: 094cd7cc9712bb7bcff1f61be467b697

No Requires field for bit64 but it depends of bit, has I said.

If I do the same thing with the CRAN version of packrat, I obtain this packrat.lock file:

PackratFormat: 1.4
PackratVersion: 0.4.8.1
RVersion: 3.2.3
Repos: CRAN=http://cran.rstudio.com/

Package: bit
Source: CRAN
Version: 1.1-12
Hash: a4cdb11cf9fd6dd38f9f40c413b81e93

Package: bit64
Source: CRAN
Version: 0.9-5
Hash: efc07a32b683ff0c778c2c6868bfb655
Requires: bit

Package: packrat
Source: CRAN
Version: 0.4.8-1
Hash: 6ad605ba7b4b476d84be6632393f5765

Is my use case too specific? Can you consider adding an option as I asked previously?

Thanks

[Valdimus]

Fix by #391