- using R Under development (unstable) (2024-07-08 r86886 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'fdasrvf/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'fdasrvf' version '2.2.0'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'fdasrvf' can be installed ... OK
See the install log for details.
- used C++ compiler: 'g++.exe (GCC) 13.2.0'
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s] OK
- checking whether the package can be unloaded cleanly ... [1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s] OK
- checking whether the namespace can be unloaded cleanly ... [1s] OK
- checking loading without being on the library search path ... [1s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [22s] OK
- checking Rd files ... [2s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
elastic.logistic.Rd: foreach
elastic.mlogistic.Rd: foreach
elastic.regression.Rd: foreach
multiple_align_functions.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of 'data' directory ... OK
- checking data for non-ASCII characters ... [1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking examples ... [15s] ERROR
Running examples in 'fdasrvf-Ex.R' failed
The error most likely occurred in:
> ### Name: pair_align_functions_bayes
> ### Title: Align two functions
> ### Aliases: pair_align_functions_bayes
> ### Keywords: bayesian
>
> ### ** Examples
>
> out <- pair_align_functions_bayes(
+ f1 = simu_data$f[, 1],
+ f2 = simu_data$f[, 2],
+ timet = simu_data$time
+ )
Resampling as number of points on q function = 101 is not a multiple of times = 5.
Error in .Call("dpcode", PACKAGE = "fdasrvf", q1, q1L, q2L, times, cut) :
"dpcode" not available for .Call() for package "fdasrvf"
Calls: pair_align_functions_bayes -> dpcode
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [15s] ERROR
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> if (requireNamespace("testthat", quietly = TRUE)){
+ library(fdasrvf)
+
+ testthat::test_check("fdasrvf")
+ testthat::snapshot_accept(files = NULL, path = "testthat")
+ } else{
+ stop("Need testthat to run checks")
+ }
i Initializing...
i Aligning 21 functions in SRVF space to 3 fPCA components...
i Starting iteration 1...
i Starting iteration 2...
i Starting iteration 3...
i Starting iteration 4...
i Starting iteration 5...
[1] 0.15604919 0.06564122 0.03321528 0.03182538 0.00000000 0.00000000
[7] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[13] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[19] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[25] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[31] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[37] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[43] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[49] 0.00000000 0.00000000 0.00000000
i Using lambda = 0
i Initializing...
i Computing Karcher mean of 21 functions in SRSF space...
i Entering iteration 1...
! The argument `x` is of class <fdawarp> but has not been
computed using the median as centroid type.
i Rerunning `time_warping()` with `centroid_type = "median"`...
i Using lambda = 0
i Initializing...
i Computing Karcher median of 21 functions in SRSF space...
i Entering iteration 1...
! The argument `x` is of class <fdawarp> but has not been
computed using the median as centroid type.
i Rerunning `time_warping()` with `centroid_type = "median"`...
i Using lambda = 0
i Initializing...
i Computing Karcher median of 21 functions in SRSF space...
i Entering iteration 1...
i Using lambda = 0
i Initializing...
i Computing Karcher mean of 21 functions in SRSF space...
i Entering iteration 1...
! The maximal number of iterations has been reached.
[ FAIL 7 | WARN 0 | SKIP 4 | PASS 79 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-align-fpca.R:21:3', 'test-boxplot.R:36:3',
'test-kmeans.R:25:3', 'test-time-warping.R:30:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_pair_align_functions_bayes.R:6:3'): Verify pair_align_functions_bayes() works as intended ──
Error in `.Call("dpcode", PACKAGE = "fdasrvf", q1, q1L, q2L, times, cut)`: "dpcode" not available for .Call() for package "fdasrvf"
Backtrace:
▆
1. └─fdasrvf::pair_align_functions_bayes(...) at test_pair_align_functions_bayes.R:6:3
2. └─fdasrvf:::dpcode(qt1_5[row], qt1_5, qt2_5, times, cut)
── Error ('test_pair_align_functions_expomap.R:10:3'): Verify pair_align_functions_expomap() works as intended ──
Error in `.Call("order_l2norm", PACKAGE = "fdasrvf", x, y)`: "order_l2norm" not available for .Call() for package "fdasrvf"
Backtrace:
▆
1. └─fdasrvf::pair_align_functions_expomap(...) at test_pair_align_functions_expomap.R:10:3
2. └─fdasrvf:::f.exp1(...)
3. ├─fdasrvf:::calcY(f.L2norm(g), g$y)
4. └─fdasrvf:::f.L2norm(g)
5. └─fdasrvf:::order_l2norm(f$x, f$y)
── Error ('test_pair_align_functions_expomap.R:59:3'): Verify init.coef arguments work correctly ──
Error in `.Call("order_l2norm", PACKAGE = "fdasrvf", x, y)`: "order_l2norm" not available for .Call() for package "fdasrvf"
Backtrace:
▆
1. └─fdasrvf::pair_align_functions_expomap(...) at test_pair_align_functions_expomap.R:59:3
2. └─fdasrvf:::f.exp1(...)
3. ├─fdasrvf:::calcY(f.L2norm(g), g$y)
4. └─fdasrvf:::f.L2norm(g)
5. └─fdasrvf:::order_l2norm(f$x, f$y)
── Error ('test_pair_align_functions_expomap.R:91:3'): Check calcY() works as intended ──
Error in `.Call("calcY", PACKAGE = "fdasrvf", area, gy)`: "calcY" not available for .Call() for package "fdasrvf"
Backtrace:
▆
1. ├─testthat::expect_equal(sum(fdasrvf:::calcY(2, 0:2)), 0.1155056305) at test_pair_align_functions_expomap.R:91:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─fdasrvf:::calcY(2, 0:2)
── Error ('test_pair_align_functions_expomap.R:96:3'): Check cuL2norm2() works as intended ──
Error in `.Call("cuL2norm2", PACKAGE = "fdasrvf", x, y)`: "cuL2norm2" not available for .Call() for package "fdasrvf"
Backtrace:
▆
1. ├─testthat::expect_equal(prod(fdasrvf:::cuL2norm2(0:2, 1:3)), 22.5) at test_pair_align_functions_expomap.R:96:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─fdasrvf:::cuL2norm2(0:2, 1:3)
── Error ('test_pair_align_functions_expomap.R:102:3'): Check trapzCpp() works as intended ──
Error in `.Call("trapzCpp", PACKAGE = "fdasrvf", x, y)`: "trapzCpp" not available for .Call() for package "fdasrvf"
Backtrace:
▆
1. ├─testthat::expect_equal(fdasrvf:::trapzCpp(0:2, 1:3), 4) at test_pair_align_functions_expomap.R:102:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─fdasrvf:::trapzCpp(0:2, 1:3)
── Error ('test_pair_align_functions_expomap.R:108:3'): Check order_l2norm() works as intended ──
Error in `.Call("order_l2norm", PACKAGE = "fdasrvf", x, y)`: "order_l2norm" not available for .Call() for package "fdasrvf"
Backtrace:
▆
1. ├─testthat::expect_equal(fdasrvf:::order_l2norm(0:2, 1:3), 3) at test_pair_align_functions_expomap.R:108:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─fdasrvf:::order_l2norm(0:2, 1:3)
[ FAIL 7 | WARN 0 | SKIP 4 | PASS 79 ]
Error: Test failures
Execution halted
- checking PDF version of manual ... [24s] OK
- checking HTML version of manual ... [14s] OK
- DONE
Status: 2 ERRORs, 1 NOTE