Error adding packrat to existing project on MacOSX

I get an error when trying to add packrat to my existing project on MacOSX 10.11 and latest R installed from homebrew. The project is available here: https://github.com/alepulver/my-thesis

packrat::init()
Initializing packrat project in directory:
- "~/Google Drive/my-thesis/analysis-in-r"
Error in isNamespaceLoaded(pkg) : 
  attempt to use zero-length variable name
In addition: There were 16 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/comparacion_cottle.Rmd'
2: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/exploratorio.Rmd'
3: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/figuras_poster.Rmd'
4: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/fragmentos_no_utilizados.Rmd'
5: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/machine_learning_analisis.Rmd'
6: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/machine_learning_pruebas.Rmd'
7: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/modelos_cottle.Rmd'
8: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/modelos_hipotesis_especificas.Rmd'
9: In value[[3L]](cond) :
  Failed to parse /var/folders/f1/64_sc7dn0_v3vh7gbwrc0vvw0000gp/T//Rtmp0m4P7K/file49307e41f209 ; dependencies in this file will not be discovered.
10: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/modelos_hipotesis_primarias.Rmd'
11: In value[[3L]](cond) :
  Failed to parse /var/folders/f1/64_sc7dn0_v3vh7gbwrc0vvw0000gp/T//Rtmp0m4P7K/file4930410c731e ; dependencies in this file will not be discovered.
12: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/template_colores.Rmd'
13: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/template_cottle.Rmd'
14: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/template_dedicacion.Rmd'
15: In readLines(file) :
  incomplete final line found on '/Users/alejandropulver/Google Drive/my-thesis/analysis-in-r/template_ubicacion_xy.Rmd'
16: In FUN(X[[i]], ...) : Package '' not available in repository or locally

Reproduce the failure by running packrat::init() in the linked my-thesis project, then inspect the reported Rmd files and the dependency-discovery warnings. Trace the zero-length variable error and failed package detection through packrat's initialization entry point. Done means initialization completes without the error and dependencies are discovered appropriately.