Running examples in 'jackstraw-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lfa.corpcor
> ### Title: Logistic Factor Analysis without C++ Dependency
> ### Aliases: lfa.corpcor
> 
> ### ** Examples
> 
> set.seed(1234)
> ## simulate genotype data from a logistic factor model
> m=5000; n=100; pi0=.9
> m0 = round(m*pi0)
> m1 = m-round(m*pi0)
> B = matrix(0, nrow=m, ncol=1)
> B[1:m1,] = matrix(runif(m1*n, min=-.5, max=.5), nrow=m1, ncol=1)
Error in matrix(runif(m1 * n, min = -0.5, max = 0.5), nrow = m1, ncol = 1) : 
  data length differs from size of matrix: [50000 != 500 x 1]
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'jackstraw.Rnw' using knitr
Warning: code chunks must not depend on the uncached chunk "sim_pca_data"
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_data'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_PA'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_1pc'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_jackstraw'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_pvalues'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_lfa_data'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Quitting from lines 123-142 (jackstraw.Rnw) 
Error: processing vignette 'jackstraw.Rnw' failed with diagnostics:
data length differs from size of matrix: [250000 != 2500 x 1]
--- failed re-building 'jackstraw.Rnw'

SUMMARY: processing the following file failed:
  'jackstraw.Rnw'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘jackstraw-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lfa.corpcor
> ### Title: Logistic Factor Analysis without C++ Dependency
> ### Aliases: lfa.corpcor
> 
> ### ** Examples
> 
> set.seed(1234)
> ## simulate genotype data from a logistic factor model
> m=5000; n=100; pi0=.9
> m0 = round(m*pi0)
> m1 = m-round(m*pi0)
> B = matrix(0, nrow=m, ncol=1)
> B[1:m1,] = matrix(runif(m1*n, min=-.5, max=.5), nrow=m1, ncol=1)
Error in matrix(runif(m1 * n, min = -0.5, max = 0.5), nrow = m1, ncol = 1) : 
  data length differs from size of matrix: [50000 != 500 x 1]
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘jackstraw.Rnw’ using knitr
Warning: code chunks must not depend on the uncached chunk "sim_pca_data"
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_data'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_PA'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_1pc'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_jackstraw'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_pvalues'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_lfa_data'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Quitting from lines 123-142 (jackstraw.Rnw) 
Error: processing vignette 'jackstraw.Rnw' failed with diagnostics:
data length differs from size of matrix: [250000 != 2500 x 1]
--- failed re-building ‘jackstraw.Rnw’

SUMMARY: processing the following file failed:
  ‘jackstraw.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘jackstraw-Ex.R’ failed
The error most likely occurred in:

> ### Name: lfa.corpcor
> ### Title: Logistic Factor Analysis without C++ Dependency
> ### Aliases: lfa.corpcor
> 
> ### ** Examples
> 
> set.seed(1234)
> ## simulate genotype data from a logistic factor model
> m=5000; n=100; pi0=.9
> m0 = round(m*pi0)
> m1 = m-round(m*pi0)
> B = matrix(0, nrow=m, ncol=1)
> B[1:m1,] = matrix(runif(m1*n, min=-.5, max=.5), nrow=m1, ncol=1)
Error in matrix(runif(m1 * n, min = -0.5, max = 0.5), nrow = m1, ncol = 1) : 
  data length differs from size of matrix: [50000 != 500 x 1]
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘jackstraw.Rnw’ using knitr
Warning: code chunks must not depend on the uncached chunk "sim_pca_data"
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_data'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_PA'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_1pc'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_jackstraw'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_pca_pvalues'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'sim_lfa_data'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Quitting from lines 123-142 (jackstraw.Rnw) 
Error: processing vignette 'jackstraw.Rnw' failed with diagnostics:
data length differs from size of matrix: [250000 != 2500 x 1]
--- failed re-building ‘jackstraw.Rnw’

SUMMARY: processing the following file failed:
  ‘jackstraw.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘jackstraw-Ex.R’ failed
The error most likely occurred in:

> ### Name: lfa.corpcor
> ### Title: Logistic Factor Analysis without C++ Dependency
> ### Aliases: lfa.corpcor
> 
> ### ** Examples
> 
> set.seed(1234)
> ## simulate genotype data from a logistic factor model
> m=5000; n=100; pi0=.9
> m0 = round(m*pi0)
> m1 = m-round(m*pi0)
> B = matrix(0, nrow=m, ncol=1)
> B[1:m1,] = matrix(runif(m1*n, min=-.5, max=.5), nrow=m1, ncol=1)
Error in matrix(runif(m1 * n, min = -0.5, max = 0.5), nrow = m1, ncol = 1) : 
  data length differs from size of matrix: [50000 != 500 x 1]
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘jackstraw.Rnw’ using knitr
Warning: code chunks must not depend on the uncached chunk "sim_pca_data"
Quitting from lines 123-142 (jackstraw.Rnw) 
Error: processing vignette 'jackstraw.Rnw' failed with diagnostics:
data length differs from size of matrix: [250000 != 2500 x 1]
--- failed re-building ‘jackstraw.Rnw’

SUMMARY: processing the following file failed:
  ‘jackstraw.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘lfa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.