CRAN Package Check Results for Package PCRedux

Last updated on 2019-12-21 10:47:53 CET.

Check Details

Version: 1.0-2
Check: examples
Result: ERROR
    Running examples in 'PCRedux-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: encu
    > ### Title: A function to calculate numerous features from amplification
    > ### curve data from a quantitative PCR experiment.
    > ### Aliases: encu
    > ### Keywords: intercept normalization preprocessing slope
    >
    > ### ** Examples
    >
    >
    > # Calculate curve features of an amplification curve data. Note that not all
    > # available CPU cores are used. If need set "all" to use all available cores.
    > # In this example the testdat data set from the qpcR package is used.
    > # The samples F1.1 and F1.2 are positive amplification curves. The samples
    > # F1.3 and F1.4 are negative.
    >
    > library(qpcR)
    Loading required package: MASS
    Loading required package: minpack.lm
    Loading required package: rgl
    Loading required package: robustbase
    Loading required package: Matrix
    > res_encu <- encu(testdat[, 1:3])
    Loading required package: bcp
    Loading required package: grid
    Error in cor.test.default(cycle_RFU[!is.na(cycle_RFU_n)], cycle_RFU_n[!is.na(cycle_RFU_n)], :
     not enough finite observations
    Calls: encu ... pcrfit_single -> <Anonymous> -> <Anonymous> -> cor.test.default
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0-2
Check: tests
Result: ERROR
     Running 'spelling.R' [0s/1s]
     Running 'testthat.R' [8s/11s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(PCRedux)
     >
     > test_check("PCRedux")
     -- 1. Error: encu is a function to calculate numerous features from amplificatio
     not enough finite observations
     Backtrace:
     1. PCRedux::encu(testdat[, 1:2])
     3. pbapply::pblapply(...)
     4. base::lapply(X, FUN, ...)
     5. PCRedux:::FUN(X[[i]], ...)
     6. PCRedux::pcrfit_single(data_RFU[, ith_run])
     7. PCRedux::autocorrelation_test(y = dat_smoothed)
     9. stats:::cor.test.default(...)
    
     -- 2. Error: pcrfit_single gives the correct dimensions and properties (@test_pc
     not enough finite observations
     Backtrace:
     1. PCRedux::pcrfit_single(RAS002[, 2])
     2. PCRedux::autocorrelation_test(y = dat_smoothed)
     4. stats:::cor.test.default(...)
    
     == testthat results ===========================================================
     [ OK: 46 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
     1. Error: encu is a function to calculate numerous features from amplification curve data from a quantitative PCR experiment (@test_encu.R#7)
     2. Error: pcrfit_single gives the correct dimensions and properties (@test_pcrfit_single.R#6)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0-2
Check: tests
Result: ERROR
     Running ‘spelling.R’ [0s/1s]
     Running ‘testthat.R’ [6s/9s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(PCRedux)
     >
     > test_check("PCRedux")
     ── 1. Error: encu is a function to calculate numerous features from amplificatio
     not enough finite observations
     Backtrace:
     1. PCRedux::encu(testdat[, 1:2])
     3. pbapply::pblapply(...)
     4. base::lapply(X, FUN, ...)
     5. PCRedux:::FUN(X[[i]], ...)
     6. PCRedux::pcrfit_single(data_RFU[, ith_run])
     7. PCRedux::autocorrelation_test(y = dat_smoothed)
     9. stats:::cor.test.default(...)
    
     ── 2. Error: pcrfit_single gives the correct dimensions and properties (@test_pc
     not enough finite observations
     Backtrace:
     1. PCRedux::pcrfit_single(RAS002[, 2])
     2. PCRedux::autocorrelation_test(y = dat_smoothed)
     4. stats:::cor.test.default(...)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 46 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
     1. Error: encu is a function to calculate numerous features from amplification curve data from a quantitative PCR experiment (@test_encu.R#7)
     2. Error: pcrfit_single gives the correct dimensions and properties (@test_pcrfit_single.R#6)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0-2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: dependencies in R code
Result: NOTE
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: S3 generic/method consistency
Result: WARN
    No protocol specified
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: replacement functions
Result: WARN
    No protocol specified
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: foreign function calls
Result: NOTE
    No protocol specified
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: R code for possible problems
Result: NOTE
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: for missing documentation entries
Result: WARN
    No protocol specified
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: for code/documentation mismatches
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-2
Check: Rd \usage sections
Result: NOTE
    No protocol specified
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64