Last updated on 2020-08-07 01:50:20 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| gam | 2 | 10 | |
| gamsel | 12 | ||
| glmnet | 1 | 11 | |
| ISLR | 12 | ||
| lars | 12 | ||
| mda | 12 | ||
| ProDenICA | 12 | ||
| softImpute | 12 | ||
| sparsenet | 12 | ||
| svmpath | 12 |
Current CRAN status: ERROR: 2, OK: 10
Version: 1.20
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Testing an2
Testing step1
── 3. Failure: (unknown) (@test_example.R#34) ─────────────────────────────────
objects[[x]] not equal to expected[[x]].
Component "anova": Component "From": 'current' is not a factor
Component "anova": Component "To": 'current' is not a factor
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 7 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ]
1. Failure: (unknown) (@test_example.R#34)
2. Failure: (unknown) (@test_example.R#34)
3. Failure: (unknown) (@test_example.R#34)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.20
Check: running tests for arch ‘i386’
Result: ERROR
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(gam)
Loading required package: splines
Loading required package: foreach
Loaded gam 1.20
>
> test_check("gam")
Start: y ~ s(x, 6) + z; AIC= 43.7495
Step:1 y ~ s(x, 6) ; AIC= 42.6681
Testing fit1
-- 1. Failure: (unknown) (@test_example.R#34) ---------------------------------
objects[[x]] not equal to expected[[x]].
Component "family": Component "initialize": Modes of target, current: expression, call
Component "family": Component "initialize": target, current do not match when deparsed
Testing fit2
Testing fit3
-- 2. Failure: (unknown) (@test_example.R#34) ---------------------------------
objects[[x]] not equal to expected[[x]].
Component "family": Component "initialize": Modes of target, current: expression, call
Component "family": Component "initialize": target, current do not match when deparsed
Testing fit4
Testing fit5
Testing fit6
Testing sum1
Testing an1
Testing an2
Testing step1
-- 3. Failure: (unknown) (@test_example.R#34) ---------------------------------
objects[[x]] not equal to expected[[x]].
Component "anova": Component "From": 'current' is not a factor
Component "anova": Component "To": 'current' is not a factor
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ]
1. Failure: (unknown) (@test_example.R#34)
2. Failure: (unknown) (@test_example.R#34)
3. Failure: (unknown) (@test_example.R#34)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.20
Check: running tests for arch ‘x64’
Result: ERROR
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(gam)
Loading required package: splines
Loading required package: foreach
Loaded gam 1.20
>
> test_check("gam")
Start: y ~ s(x, 6) + z; AIC= 43.7495
Step:1 y ~ s(x, 6) ; AIC= 42.6681
Testing fit1
-- 1. Failure: (unknown) (@test_example.R#34) ---------------------------------
objects[[x]] not equal to expected[[x]].
Component "family": Component "initialize": Modes of target, current: expression, call
Component "family": Component "initialize": target, current do not match when deparsed
Testing fit2
Testing fit3
-- 2. Failure: (unknown) (@test_example.R#34) ---------------------------------
objects[[x]] not equal to expected[[x]].
Component "family": Component "initialize": Modes of target, current: expression, call
Component "family": Component "initialize": target, current do not match when deparsed
Testing fit4
Testing fit5
Testing fit6
Testing sum1
Testing an1
Testing an2
Testing step1
-- 3. Failure: (unknown) (@test_example.R#34) ---------------------------------
objects[[x]] not equal to expected[[x]].
Component "anova": Component "From": 'current' is not a factor
Component "anova": Component "To": 'current' is not a factor
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ]
1. Failure: (unknown) (@test_example.R#34)
2. Failure: (unknown) (@test_example.R#34)
3. Failure: (unknown) (@test_example.R#34)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 12
Current CRAN status: ERROR: 1, OK: 11
Version: 4.0-2
Check: examples
Result: ERROR
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:
> ### Name: glmnet
> ### Title: fit a GLM with lasso or elasticnet regularization
> ### Aliases: glmnet relax.glmnet
> ### Keywords: models regression
>
> ### ** Examples
>
>
> # Gaussian
> x = matrix(rnorm(100 * 20), 100, 20)
> y = rnorm(100)
> fit1 = glmnet(x, y)
> print(fit1)
Call: glmnet(x = x, y = y)
Df %Dev Lambda
1 0 0.00 0.197600
2 1 0.60 0.180000
3 1 1.10 0.164000
4 2 1.54 0.149500
5 4 2.79 0.136200
6 4 4.06 0.124100
7 4 5.11 0.113100
8 4 5.98 0.103000
9 5 6.78 0.093870
10 5 7.52 0.085530
11 6 8.20 0.077940
12 6 8.91 0.071010
13 6 9.49 0.064700
14 8 10.07 0.058960
15 9 10.60 0.053720
16 10 11.12 0.048950
17 12 11.57 0.044600
18 12 11.97 0.040640
19 12 12.31 0.037030
20 13 12.59 0.033740
21 13 12.88 0.030740
22 14 13.13 0.028010
23 14 13.35 0.025520
24 14 13.54 0.023250
25 14 13.69 0.021190
26 14 13.82 0.019310
27 14 13.93 0.017590
28 14 14.02 0.016030
29 14 14.09 0.014600
30 14 14.15 0.013310
31 15 14.20 0.012120
32 17 14.25 0.011050
33 17 14.28 0.010070
34 17 14.32 0.009172
35 18 14.34 0.008357
36 19 14.36 0.007614
37 19 14.39 0.006938
38 19 14.40 0.006322
39 19 14.42 0.005760
40 20 14.43 0.005248
41 20 14.44 0.004782
42 20 14.45 0.004357
43 20 14.46 0.003970
44 20 14.47 0.003617
45 20 14.48 0.003296
46 20 14.48 0.003003
47 20 14.49 0.002736
48 20 14.49 0.002493
49 20 14.49 0.002272
50 20 14.50 0.002070
51 20 14.50 0.001886
52 20 14.50 0.001719
53 20 14.50 0.001566
54 20 14.50 0.001427
55 20 14.50 0.001300
56 20 14.50 0.001185
57 20 14.50 0.001079
58 20 14.51 0.000983
59 20 14.51 0.000896
60 20 14.51 0.000816
61 20 14.51 0.000744
62 20 14.51 0.000678
63 20 14.51 0.000618
64 20 14.51 0.000563
65 20 14.51 0.000513
66 20 14.51 0.000467
> coef(fit1, s = 0.01) # extract coefficients at a single value of lambda
21 x 1 sparse Matrix of class "dgCMatrix"
1
(Intercept) -0.1154251627
V1 0.1003781671
V2 0.2123146104
V3 0.1478378877
V4 0.0071738140
V5 0.0017068814
V6 .
V7 -0.0009736938
V8 -0.1988997621
V9 .
V10 0.1071297719
V11 0.0563547748
V12 0.0392889072
V13 -0.1673111781
V14 -0.0331802879
V15 0.0322438934
V16 0.0368881782
V17 .
V18 0.0013228366
V19 0.0613253373
V20 0.0388175403
> predict(fit1, newx = x[1:10, ], s = c(0.01, 0.005)) # make predictions
1 2
[1,] 0.1623437 0.1923152
[2,] -0.5447409 -0.5540136
[3,] 0.3089815 0.3238559
[4,] 0.3441108 0.3593363
[5,] -0.4261315 -0.4431612
[6,] 0.4629769 0.4778225
[7,] 0.5536940 0.5777430
[8,] 0.3760726 0.3938430
[9,] -0.5032892 -0.5408060
[10,] -0.3201688 -0.3367624
>
> # Relaxed
> fit1r = glmnet(x, y, relax = TRUE) # can be used with any model
>
> # multivariate gaussian
> y = matrix(rnorm(100 * 3), 100, 3)
> fit1m = glmnet(x, y, family = "mgaussian")
> plot(fit1m, type.coef = "2norm")
>
> # binomial
> g2 = sample(c(0,1), 100, replace = TRUE)
> fit2 = glmnet(x, g2, family = "binomial")
> fit2n = glmnet(x, g2, family = binomial(link=cloglog))
Error in elnet.fit(x, z, w, lambda, alpha, intercept, thresh = thresh, :
NA/NaN/Inf in foreign function call (arg 25)
Calls: glmnet -> glmnet.path -> glmnet.fit -> elnet.fit
Execution halted
Flavor: r-patched-solaris-x86
Version: 4.0-2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘Coxnet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
(process:16066): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9'
(process:16066): Pango-WARNING **: font_face status is: <unknown error status>
(process:16066): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)
(process:16066): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9', text='m'
--- finished re-building ‘Coxnet.Rmd’
--- re-building ‘glmnet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: lars
Loaded lars 1.2
--- finished re-building ‘glmnet.Rmd’
--- re-building ‘glmnetFamily.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: Matrix
Loaded glmnet 4.0-2
Quitting from lines 121-124 (glmnetFamily.Rmd)
Error: processing vignette 'glmnetFamily.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 25)
--- failed re-building ‘glmnetFamily.Rmd’
--- re-building ‘relax.Rmd’ using rmarkdown
Warning in engine$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 ‘relax.Rmd’
SUMMARY: processing the following file failed:
‘glmnetFamily.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Current CRAN status: OK: 12
Current CRAN status: NOTE: 12
Version: 1.2
Check: R code for possible problems
Result: NOTE
betabreaker: no visible global function definition for 'predict'
coef.lars: no visible global function definition for 'predict'
cv.lars: no visible global function definition for 'predict'
cv.lars: no visible binding for global variable 'var'
error.bars: no visible global function definition for 'segments'
plot.lars: no visible global function definition for 'matplot'
plot.lars: no visible global function definition for 'title'
plot.lars: no visible global function definition for 'abline'
plot.lars: no visible global function definition for 'axis'
predict.lars: no visible global function definition for 'approx'
Undefined global functions or variables:
abline approx axis matplot predict segments title var
Consider adding
importFrom("graphics", "abline", "axis", "matplot", "segments",
"title")
importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64
Version: 1.2
Check: Rd line widths
Result: NOTE
Rd file 'cv.lars.Rd':
\usage lines wider than 90 characters:
trace = FALSE, plot.it = TRUE, se = TRUE,type = c("lasso", "lar", "forward.stagewise", "stepwise"),
Rd file 'lars.Rd':
\usage lines wider than 90 characters:
trace = FALSE, normalize = TRUE, intercept = TRUE, Gram, eps = .Machine$double.eps, max.steps, use.Gram = TRUE)
Rd file 'plot.lars.Rd':
\usage lines wider than 90 characters:
plot(x, xvar= c("norm", "df", "arc.length", "step"), breaks = TRUE, plottype = c("coefficients",
These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.2
Check: compiled code
Result: NOTE
File ‘lars/libs/lars.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2
Check: R code for possible problems
Result: NOTE
betabreaker: no visible global function definition for ‘predict’
coef.lars: no visible global function definition for ‘predict’
cv.lars: no visible global function definition for ‘predict’
cv.lars: no visible binding for global variable ‘var’
error.bars: no visible global function definition for ‘segments’
plot.lars: no visible global function definition for ‘plot’
plot.lars: no visible global function definition for ‘matplot’
plot.lars: no visible global function definition for ‘title’
plot.lars: no visible global function definition for ‘abline’
plot.lars: no visible global function definition for ‘axis’
plotCVLars: no visible global function definition for ‘plot’
predict.lars: no visible global function definition for ‘approx’
Undefined global functions or variables:
abline approx axis matplot plot predict segments title var
Consider adding
importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
"title")
importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 12
Current CRAN status: NOTE: 12
Version: 1.0
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0
Check: R code for possible problems
Result: NOTE
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
r.gaussmix: no visible global function definition for 'rmultinom'
r.gaussmix: no visible global function definition for 'rnorm'
rjordan: no visible global function definition for 'rt'
rjordan: no visible global function definition for 'runif'
rmix.dexp: no visible global function definition for 'runif'
Undefined global functions or variables:
dnorm dt dunif fitted poisson predict residuals rmultinom rnorm rt
runif smooth.spline
Consider adding
importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
"predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
"smooth.spline")
to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64
Version: 1.0
Check: R code for possible problems
Result: NOTE
GPois: no visible global function definition for ‘dnorm’
GPois: no visible binding for global variable ‘poisson’
GPois: no visible global function definition for ‘predict’
GPois: no visible global function definition for ‘fitted’
GPois: no visible global function definition for ‘residuals’
GPois: no visible global function definition for ‘smooth.spline’
ProDenICA: no visible global function definition for ‘rnorm’
d.gaussmix: no visible global function definition for ‘dnorm’
djordan: no visible global function definition for ‘dt’
djordan: no visible global function definition for ‘dunif’
mixmat: no visible global function definition for ‘rnorm’
mixmat: no visible global function definition for ‘runif’
plot.ProDenICA: no visible global function definition for ‘plot’
r.gaussmix: no visible global function definition for ‘rmultinom’
r.gaussmix: no visible global function definition for ‘rnorm’
rjordan: no visible global function definition for ‘rt’
rjordan: no visible global function definition for ‘runif’
rmix.dexp: no visible global function definition for ‘runif’
Undefined global functions or variables:
dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
rt runif smooth.spline
Consider adding
importFrom("graphics", "plot")
importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
"predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
"smooth.spline")
to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status: NOTE: 12
Version: 1.4
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.4
Check: R code for possible problems
Result: NOTE
Ssimpute.als: no visible global function definition for 'rnorm'
Ssvd.als: no visible global function definition for 'rnorm'
cs.default: no visible binding for global variable 'weighted.mean'
simpute.als: no visible global function definition for 'rnorm'
Undefined global functions or variables:
rnorm weighted.mean
Consider adding
importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.4
Check: compiled code
Result: NOTE
File ‘softImpute/libs/softImpute.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 12
Current CRAN status: OK: 12