Last updated on 2020-05-29 10:47:29 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 11.98 | 77.23 | 89.21 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 9.31 | 60.88 | 70.19 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 120.05 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 108.73 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.1.0 | 25.00 | 117.00 | 142.00 | ERROR | |
| r-patched-linux-x86_64 | 1.1.0 | 10.95 | 77.65 | 88.60 | ERROR | |
| r-patched-solaris-x86 | 1.1.0 | 162.40 | ERROR | |||
| r-release-linux-x86_64 | 1.1.0 | 11.92 | 77.05 | 88.97 | ERROR | |
| r-release-osx-x86_64 | 1.1.0 | OK | ||||
| r-release-windows-ix86+x86_64 | 1.1.0 | 20.00 | 99.00 | 119.00 | ERROR | |
| r-oldrel-osx-x86_64 | 1.1.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.1.0 | 20.00 | 84.00 | 104.00 | ERROR |
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in 'PheCAP-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PheCAP-package
> ### Title: High-Throughput Phenotyping with EHR using a Common Automated
> ### Pipeline
> ### Aliases: PheCAP-package PheCAP
> ### Keywords: package
>
> ### ** Examples
>
> # Simulate an EHR dataset
> size <- 2000
> latent <- rgamma(size, 0.3)
> latent2 <- rgamma(size, 0.3)
> ehr_data <- data.frame(
+ ICD1 = rpois(size, 7 * (rgamma(size, 0.2) + latent) / 0.5),
+ ICD2 = rpois(size, 6 * (rgamma(size, 0.8) + latent) / 1.1),
+ ICD3 = rpois(size, 1 * rgamma(size, 0.5 + latent2) / 0.5),
+ ICD4 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
+ NLP1 = rpois(size, 8 * (rgamma(size, 0.2) + latent) / 0.6),
+ NLP2 = rpois(size, 2 * (rgamma(size, 1.1) + latent) / 1.5),
+ NLP3 = rpois(size, 5 * (rgamma(size, 0.1) + latent) / 0.5),
+ NLP4 = rpois(size, 11 * rgamma(size, 1.9 + latent) / 1.9),
+ NLP5 = rpois(size, 3 * rgamma(size, 0.5 + latent2) / 0.5),
+ NLP6 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
+ NLP7 = rpois(size, 1 * rgamma(size, 0.5) / 0.5),
+ HU = rpois(size, 30 * rgamma(size, 0.1) / 0.1),
+ label = NA)
> ii <- sample.int(size, 400)
> ehr_data[ii, "label"] <- with(
+ ehr_data[ii, ], rbinom(400, 1, plogis(
+ -5 + 1.5 * log1p(ICD1) + log1p(NLP1) +
+ 0.8 * log1p(NLP3) - 0.5 * log1p(HU))))
>
> # Define features and labels used for phenotyping.
> data <- PhecapData(ehr_data, "HU", "label", validation = 0.4)
> data
PheCAP Data
Feature: 2000 observations of 12 variables
Label: 131 yes, 269 no, 1600 missing
Size of training samples: 240
Size of validation samples: 160
>
> # Specify the surrogate used for
> # surrogate-assisted feature extraction (SAFE).
> # The typical way is to specify a main ICD code, a main NLP CUI,
> # as well as their combination.
> # The default lower_cutoff is 1, and the default upper_cutoff is 10.
> # In some cases one may want to define surrogate through lab test.
> # Feel free to change the cutoffs based on domain knowledge.
> surrogates <- list(
+ PhecapSurrogate(
+ variable_names = "ICD1",
+ lower_cutoff = 1, upper_cutoff = 10),
+ PhecapSurrogate(
+ variable_names = "NLP1",
+ lower_cutoff = 1, upper_cutoff = 10))
>
> # Run surrogate-assisted feature extraction (SAFE)
> # and show result.
> feature_selected <- phecap_run_feature_extraction(
+ data, surrogates, num_subsamples = 50, subsample_size = 200)
Error in glmnet(x, y, weights = subject_weight, family = "binomial", thresh = 5e-07, :
argument "subject_weight" is missing, with no default
Calls: phecap_run_feature_extraction ... t -> sapply -> lapply -> FUN -> fit_lasso_bic -> glmnet
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'NER-MetaMAP.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'NER-MetaMAP.Rmd'
--- re-building 'NLP-NILE.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'NLP-NILE.Rmd'
--- re-building 'example1.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 69-71 (example1.Rmd)
Error: processing vignette 'example1.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building 'example1.Rmd'
--- re-building 'example2.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 40-41 (example2.Rmd)
Error: processing vignette 'example2.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building 'example2.Rmd'
--- re-building 'main.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'main.Rmd'
SUMMARY: processing the following files failed:
'example1.Rmd' 'example2.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘PheCAP-Ex.R’ failed
The error most likely occurred in:
> ### Name: PheCAP-package
> ### Title: High-Throughput Phenotyping with EHR using a Common Automated
> ### Pipeline
> ### Aliases: PheCAP-package PheCAP
> ### Keywords: package
>
> ### ** Examples
>
> # Simulate an EHR dataset
> size <- 2000
> latent <- rgamma(size, 0.3)
> latent2 <- rgamma(size, 0.3)
> ehr_data <- data.frame(
+ ICD1 = rpois(size, 7 * (rgamma(size, 0.2) + latent) / 0.5),
+ ICD2 = rpois(size, 6 * (rgamma(size, 0.8) + latent) / 1.1),
+ ICD3 = rpois(size, 1 * rgamma(size, 0.5 + latent2) / 0.5),
+ ICD4 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
+ NLP1 = rpois(size, 8 * (rgamma(size, 0.2) + latent) / 0.6),
+ NLP2 = rpois(size, 2 * (rgamma(size, 1.1) + latent) / 1.5),
+ NLP3 = rpois(size, 5 * (rgamma(size, 0.1) + latent) / 0.5),
+ NLP4 = rpois(size, 11 * rgamma(size, 1.9 + latent) / 1.9),
+ NLP5 = rpois(size, 3 * rgamma(size, 0.5 + latent2) / 0.5),
+ NLP6 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
+ NLP7 = rpois(size, 1 * rgamma(size, 0.5) / 0.5),
+ HU = rpois(size, 30 * rgamma(size, 0.1) / 0.1),
+ label = NA)
> ii <- sample.int(size, 400)
> ehr_data[ii, "label"] <- with(
+ ehr_data[ii, ], rbinom(400, 1, plogis(
+ -5 + 1.5 * log1p(ICD1) + log1p(NLP1) +
+ 0.8 * log1p(NLP3) - 0.5 * log1p(HU))))
>
> # Define features and labels used for phenotyping.
> data <- PhecapData(ehr_data, "HU", "label", validation = 0.4)
> data
PheCAP Data
Feature: 2000 observations of 12 variables
Label: 131 yes, 269 no, 1600 missing
Size of training samples: 240
Size of validation samples: 160
>
> # Specify the surrogate used for
> # surrogate-assisted feature extraction (SAFE).
> # The typical way is to specify a main ICD code, a main NLP CUI,
> # as well as their combination.
> # The default lower_cutoff is 1, and the default upper_cutoff is 10.
> # In some cases one may want to define surrogate through lab test.
> # Feel free to change the cutoffs based on domain knowledge.
> surrogates <- list(
+ PhecapSurrogate(
+ variable_names = "ICD1",
+ lower_cutoff = 1, upper_cutoff = 10),
+ PhecapSurrogate(
+ variable_names = "NLP1",
+ lower_cutoff = 1, upper_cutoff = 10))
>
> # Run surrogate-assisted feature extraction (SAFE)
> # and show result.
> feature_selected <- phecap_run_feature_extraction(
+ data, surrogates, num_subsamples = 50, subsample_size = 200)
Error in glmnet(x, y, weights = subject_weight, family = "binomial", thresh = 5e-07, :
argument "subject_weight" is missing, with no default
Calls: phecap_run_feature_extraction ... t -> sapply -> lapply -> FUN -> fit_lasso_bic -> glmnet
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘NER-MetaMAP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘NER-MetaMAP.Rmd’
--- re-building ‘NLP-NILE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘NLP-NILE.Rmd’
--- re-building ‘example1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 69-71 (example1.Rmd)
Error: processing vignette 'example1.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building ‘example1.Rmd’
--- re-building ‘example2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 40-41 (example2.Rmd)
Error: processing vignette 'example2.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building ‘example2.Rmd’
--- re-building ‘main.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘main.Rmd’
SUMMARY: processing the following files failed:
‘example1.Rmd’ ‘example2.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘NER-MetaMAP.Rmd’ using rmarkdown
--- finished re-building ‘NER-MetaMAP.Rmd’
--- re-building ‘NLP-NILE.Rmd’ using rmarkdown
--- finished re-building ‘NLP-NILE.Rmd’
--- re-building ‘example1.Rmd’ using rmarkdown
Quitting from lines 69-71 (example1.Rmd)
Error: processing vignette 'example1.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building ‘example1.Rmd’
--- re-building ‘example2.Rmd’ using rmarkdown
Quitting from lines 40-41 (example2.Rmd)
Error: processing vignette 'example2.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building ‘example2.Rmd’
--- re-building ‘main.Rmd’ using rmarkdown
--- finished re-building ‘main.Rmd’
SUMMARY: processing the following files failed:
‘example1.Rmd’ ‘example2.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc