Last updated on 2024-04-22 20:53:36 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.4 | 436.29 | 170.21 | 606.50 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.4 | 398.36 | 174.21 | 572.57 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.0.4 | 900.45 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.4 | 1092.48 | NOTE | |||
| r-prerel-macos-arm64 | 1.0.4 | 175.00 | NOTE | |||
| r-prerel-windows-x86_64 | 1.0.4 | 330.00 | 207.00 | 537.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.4 | 490.67 | 219.92 | 710.59 | NOTE | |
| r-release-linux-x86_64 | 1.0.4 | 384.86 | 218.17 | 603.03 | NOTE | |
| r-release-macos-arm64 | 1.0.4 | 173.00 | ERROR | |||
| r-release-macos-x86_64 | 1.0.4 | 214.00 | ERROR | |||
| r-release-windows-x86_64 | 1.0.4 | 455.00 | 258.00 | 713.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0.4 | 124.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.0.4 | 454.00 | 228.00 | 682.00 | NOTE |
Version: 1.0.4
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'MicrobeDS', 'phyloseq'
Flavors: r-devel-linux-x86_64-debian-clang, r-release-macos-arm64, r-release-macos-x86_64
Version: 1.0.4
Check: Rd files
Result: NOTE
checkRd: (-1) maltipoo_fit.Rd:72: Lost braces; missing escapes or markup?
72 | Where A = (I_N + X * Gamma * X')^{-1}, K^{-1} = Xi is a (D-1)x(D-1)
| ^
checkRd: (-1) maltipoo_fit.Rd:72: Lost braces; missing escapes or markup?
72 | Where A = (I_N + X * Gamma * X')^{-1}, K^{-1} = Xi is a (D-1)x(D-1)
| ^
checkRd: (-1) maltipoo_fit.Rd:74: Lost braces; missing escapes or markup?
74 | e^{ell_i} is a scale for that variance component and Phi^{-1} is
| ^
checkRd: (-1) maltipoo_fit.Rd:74: Lost braces; missing escapes or markup?
74 | e^{ell_i} is a scale for that variance component and Phi^{-1} is
| ^
checkRd: (-1) optimMaltipooCollapsed.Rd:110: Lost braces; missing escapes or markup?
110 | Where A = (I_N + e^{ell_1}\\*X\\*U_1\\*X' + ... + e^{ell_P}\\*X\\*U_P\\*X' ),
| ^
checkRd: (-1) optimMaltipooCollapsed.Rd:110: Lost braces; missing escapes or markup?
110 | Where A = (I_N + e^{ell_1}\\*X\\*U_1\\*X' + ... + e^{ell_P}\\*X\\*U_P\\*X' ),
| ^
checkRd: (-1) optimPibbleCollapsed.Rd:45: Lost braces; missing escapes or markup?
45 | \item{AInv}{N x N precision matrix given by (I_N + X'\emph{Gamma}X)^{-1}}
| ^
checkRd: (-1) optimPibbleCollapsed.Rd:123: Lost braces; missing escapes or markup?
123 | matrix, Gamma is a Q x Q covariance matrix, and Phi^{-1} is ALRInv_D
| ^
checkRd: (-1) orthus_fit.Rd:72: Lost braces; missing escapes or markup?
72 | Where Gamma is a Q x Q covariance matrix, and Phi^{-1} is
| ^
checkRd: (-1) pibble_fit.Rd:72: Lost braces; missing escapes or markup?
72 | Where Gamma is a Q x Q covariance matrix, and Phi^{-1} is
| ^
checkRd: (-1) uncollapsePibble.Rd:66: Lost braces; missing escapes or markup?
66 | matrix, Gamma is a Q x Q covariance matrix, and Phi^{-1} is ALRInv_D
| ^
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-prerel-macos-arm64, r-prerel-windows-x86_64, r-patched-linux-x86_64
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [30s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(fido)
Attaching package: 'fido'
The following objects are masked from 'package:stats':
coef, predict
The following objects are masked from 'package:base':
as.list, print, summary
>
> #Sys.setenv(KMP_DUPLICATE_LIB_OK="TRUE")
> test_check("fido")
[1] 1.633944461 -1.263449460 -0.160491058 -0.151694924 -1.414460839
[6] 0.414752819 -0.993922266 0.192605335 1.193392223 1.208187867
[11] -0.442588541 -0.372323748 0.988703140 -0.795025503 2.192619586
[16] -0.341248035 -1.049458148 1.468107559 0.334664117 -0.271458846
[21] 0.679563767 -0.316257759 -2.037444833 -0.035804826 1.227767823
[26] -0.885689025 -0.106695203 2.066079039 0.414366039 0.037705700
[31] 0.565549634 -1.571477119 -0.382226485 0.247617015 0.007665408
[36] 0.440607554 -0.078739980 -0.250203498 -0.176178174 -0.291509535
[41] -1.991545754 0.732742452 -0.590506199 -1.240481354 -0.372671845
[46] 0.407478140 -0.273629130 -1.108338021 0.633024650 -0.158659083
[51] 0.263941695 0.214063401 0.141741788 1.198418608 0.042556410
[56] -0.289431854 -0.504657821 2.139022094 -1.023448488 0.556645664
[61] -1.841021837 0.456873518 -0.178044899 -0.257460256 -1.434609346
[66] 0.112159524 2.023069733 -0.745983224 0.701592007 0.651468327
[71] -0.252660086 1.249760504 0.412971619 0.476405230 -0.852435593
[76] 0.435228437 -1.048132400 -0.603121808 1.424949004 1.143285509
[81] 1.311087367 -1.644916843 -0.263535202 0.291603591 -1.869842768
[86] 1.903525214 -1.386759951 0.810217283 0.439084905 0.239992541
[91] -1.489189158 0.249485574 -1.651424329 1.815707370 1.286940214
[96] -1.290575099 -1.156862005 0.387003783 0.613538302 -0.726791282
$data
# A tibble: 16 × 9
Parameter coord covariate val .lower .upper .width .point .interval
<chr> <fct> <fct> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 Lambda clr_c1 x1 4.58 4.34 4.84 0.5 mean qi
2 Lambda clr_c1 x2 -1.47 -1.78 -1.14 0.5 mean qi
3 Lambda clr_c2 x1 -6.50 -7.04 -5.92 0.5 mean qi
4 Lambda clr_c2 x2 -0.0560 -0.525 0.409 0.5 mean qi
5 Lambda clr_c1 x1 4.58 4.10 5.05 0.8 mean qi
6 Lambda clr_c1 x2 -1.47 -2.06 -0.861 0.8 mean qi
7 Lambda clr_c2 x1 -6.50 -7.57 -5.46 0.8 mean qi
8 Lambda clr_c2 x2 -0.0560 -0.929 0.855 0.8 mean qi
9 Lambda clr_c1 x1 4.58 3.82 5.31 0.95 mean qi
10 Lambda clr_c1 x2 -1.47 -2.39 -0.598 0.95 mean qi
11 Lambda clr_c2 x1 -6.50 -8.10 -4.92 0.95 mean qi
12 Lambda clr_c2 x2 -0.0560 -1.45 1.38 0.95 mean qi
13 Lambda clr_c1 x1 4.58 3.60 5.52 0.99 mean qi
14 Lambda clr_c1 x2 -1.47 -2.64 -0.294 0.99 mean qi
15 Lambda clr_c2 x1 -6.50 -8.71 -4.38 0.99 mean qi
16 Lambda clr_c2 x2 -0.0560 -1.92 1.81 0.99 mean qi
$layers
$layers[[1]]
geom_interval: orientation = NA, interval_size_range = c(1, 6), interval_size_domain = c(1, 6), arrow = NULL, na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
$layers[[2]]
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
$scales
<ggproto object: Class ScalesList, gg>
add: function
add_defaults: function
add_missing: function
backtransform_df: function
clone: function
find: function
get_scales: function
has_scale: function
input: function
map_df: function
n: function
non_position_scales: function
scales: list
train_df: function
transform_df: function
super: <ggproto object: Class ScalesList, gg>
$guides
<Guides[1] ggproto object>
colour : <GuideLegend>
$mapping
Aesthetic mapping:
* `x` -> `.data$val`
* `y` -> `.data$coord`
* `xmin` -> `.lower`
* `xmax` -> `.upper`
$theme
List of 136
$ line :List of 6
..$ colour : chr "black"
..$ linewidth : num 0.5
..$ linetype : num 1
..$ lineend : chr "butt"
..$ arrow : logi FALSE
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_line" "element"
$ rect :List of 5
..$ fill : chr "white"
..$ colour : chr "black"
..$ linewidth : num 0.5
..$ linetype : num 1
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_rect" "element"
$ text :List of 11
..$ family : chr ""
..$ face : chr "plain"
..$ colour : chr "black"
..$ size : num 11
..$ hjust : num 0.5
..$ vjust : num 0.5
..$ angle : num 0
..$ lineheight : num 0.9
..$ margin : 'margin' num [1:4] 0points 0points 0points 0points
.. ..- attr(*, "unit")= int 8
..$ debug : logi FALSE
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ title : NULL
$ aspect.ratio : NULL
$ axis.title : NULL
$ axis.title.x :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : NULL
..$ vjust : num 1
..$ angle : NULL
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 2.75points 0points 0points 0points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.title.x.top :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : NULL
..$ vjust : num 0
..$ angle : NULL
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 0points 0points 2.75points 0points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.title.x.bottom : NULL
$ axis.title.y : list()
..- attr(*, "class")= chr [1:2] "element_blank" "element"
$ axis.title.y.left : NULL
$ axis.title.y.right :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : NULL
..$ vjust : num 1
..$ angle : num -90
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 0points 0points 0points 2.75points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.text :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : chr "grey30"
..$ size : 'rel' num 0.8
..$ hjust : NULL
..$ vjust : NULL
..$ angle : NULL
..$ lineheight : NULL
..$ margin : NULL
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.text.x :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : NULL
..$ vjust : num 1
..$ angle : NULL
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 2.2points 0points 0points 0points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.text.x.top :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : NULL
..$ vjust : num 0
..$ angle : NULL
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 0points 0points 2.2points 0points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.text.x.bottom : NULL
$ axis.text.y :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : num 1
..$ vjust : NULL
..$ angle : NULL
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 0points 2.2points 0points 0points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.text.y.left : NULL
$ axis.text.y.right :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : num 0
..$ vjust : NULL
..$ angle : NULL
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 0points 0points 0points 2.2points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.text.theta : NULL
$ axis.text.r :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : num 0.5
..$ vjust : NULL
..$ angle : NULL
..$ lineheight : NULL
..$ margin : 'margin' num [1:4] 0points 2.2points 0points 2.2points
.. ..- attr(*, "unit")= int 8
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ axis.ticks : list()
..- attr(*, "class")= chr [1:2] "element_blank" "element"
$ axis.ticks.x : NULL
$ axis.ticks.x.top : NULL
$ axis.ticks.x.bottom : NULL
$ axis.ticks.y : NULL
$ axis.ticks.y.left : NULL
$ axis.ticks.y.right : NULL
$ axis.ticks.theta : NULL
$ axis.ticks.r : NULL
$ axis.minor.ticks.x.top : NULL
$ axis.minor.ticks.x.bottom : NULL
$ axis.minor.ticks.y.left : NULL
$ axis.minor.ticks.y.right : NULL
$ axis.minor.ticks.theta : NULL
$ axis.minor.ticks.r : NULL
$ axis.ticks.length : 'simpleUnit' num 2.75points
..- attr(*, "unit")= int 8
$ axis.ticks.length.x : NULL
$ axis.ticks.length.x.top : NULL
$ axis.ticks.length.x.bottom : NULL
$ axis.ticks.length.y : NULL
$ axis.ticks.length.y.left : NULL
$ axis.ticks.length.y.right : NULL
$ axis.ticks.length.theta : NULL
$ axis.ticks.length.r : NULL
$ axis.minor.ticks.length : 'rel' num 0.75
$ axis.minor.ticks.length.x : NULL
$ axis.minor.ticks.length.x.top : NULL
$ axis.minor.ticks.length.x.bottom: NULL
$ axis.minor.ticks.length.y : NULL
$ axis.minor.ticks.length.y.left : NULL
$ axis.minor.ticks.length.y.right : NULL
$ axis.minor.ticks.length.theta : NULL
$ axis.minor.ticks.length.r : NULL
$ axis.line : list()
..- attr(*, "class")= chr [1:2] "element_blank" "element"
$ axis.line.x : NULL
$ axis.line.x.top : NULL
$ axis.line.x.bottom : NULL
$ axis.line.y : NULL
$ axis.line.y.left : NULL
$ axis.line.y.right : NULL
$ axis.line.theta : NULL
$ axis.line.r : NULL
$ legend.background : list()
..- attr(*, "class")= chr [1:2] "element_blank" "element"
$ legend.margin : 'margin' num [1:4] 5.5points 5.5points 5.5points 5.5points
..- attr(*, "unit")= int 8
$ legend.spacing : 'simpleUnit' num 11points
..- attr(*, "unit")= int 8
$ legend.spacing.x : NULL
$ legend.spacing.y : NULL
$ legend.key : list()
..- attr(*, "class")= chr [1:2] "element_blank" "element"
$ legend.key.size : 'simpleUnit' num 1.2lines
..- attr(*, "unit")= int 3
$ legend.key.height : NULL
$ legend.key.width : NULL
$ legend.key.spacing : 'simpleUnit' num 5.5points
..- attr(*, "unit")= int 8
$ legend.key.spacing.x : NULL
$ legend.key.spacing.y : NULL
$ legend.frame : NULL
$ legend.ticks : NULL
$ legend.ticks.length : 'rel' num 0.2
$ legend.axis.line : NULL
$ legend.text :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : 'rel' num 0.8
..$ hjust : NULL
..$ vjust : NULL
..$ angle : NULL
..$ lineheight : NULL
..$ margin : NULL
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ legend.text.position : NULL
$ legend.title :List of 11
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : num 0
..$ vjust : NULL
..$ angle : NULL
..$ lineheight : NULL
..$ margin : NULL
..$ debug : NULL
..$ inherit.blank: logi TRUE
..- attr(*, "class")= chr [1:2] "element_text" "element"
$ legend.title.position : NULL
$ legend.position : chr "right"
$ legend.position.inside : NULL
$ legend.direction : NULL
$ legend.byrow : NULL
$ legend.justification : chr "center"
$ legend.justification.top : NULL
$ legend.justification.bottom : NULL
$ legend.justification.left : NULL
$ legend.justification.right : NULL
$ legend.justification.inside : NULL
$ legend.location : NULL
$ legend.box : NULL
$ legend.box.just : NULL
$ legend.box.margin : 'margin' num [1:4] 0cm 0cm 0cm 0cm
..- attr(*, "unit")= int 1
$ legend.box.background : list()
..- attr(*, "class")= chr [1:2] "element_blank" "element"
$ legend.box.spacing : 'simpleUnit' num 11points
..- attr(*, "unit")= int 8
[list output truncated]
- attr(*, "class")= chr [1:2] "theme" "gg"
- attr(*, "complete")= logi TRUE
- attr(*, "validate")= logi TRUE
$coordinates
<ggproto object: Class CoordCartesian, Coord, gg>
aspect: function
backtransform_range: function
clip: on
default: TRUE
distance: function
expand: TRUE
is_free: function
is_linear: function
labels: function
limits: list
modify_scales: function
range: function
render_axis_h: function
render_axis_v: function
render_bg: function
render_fg: function
setup_data: function
setup_layout: function
setup_panel_guides: function
setup_panel_params: function
setup_params: function
train_panel_guides: function
transform: function
super: <ggproto object: Class CoordCartesian, Coord, gg>
$facet
<ggproto object: Class FacetGrid, Facet, gg>
compute_layout: function
draw_back: function
draw_front: function
draw_labels: function
draw_panels: function
finish_data: function
init_scales: function
map_data: function
params: list
setup_data: function
setup_params: function
shrink: TRUE
train_scales: function
vars: function
super: <ggproto object: Class FacetGrid, Facet, gg>
$plot_env
<environment: 0x55e393aec480>
$layout
<ggproto object: Class Layout, gg>
coord: NULL
coord_params: list
facet: NULL
facet_params: list
finish_data: function
get_scales: function
layout: NULL
map_position: function
panel_params: NULL
panel_scales_x: NULL
panel_scales_y: NULL
render: function
render_labels: function
reset_scales: function
resolve_label: function
setup: function
setup_panel_guides: function
setup_panel_params: function
train_position: function
super: <ggproto object: Class Layout, gg>
$labels
$labels$x
[1] "Log-Ratio Value"
$labels$y
[1] "coord"
$labels$xmin
[1] ".lower"
$labels$xmax
[1] ".upper"
attr(,"class")
[1] "gg" "ggplot"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ilr.R:11:3'): clr plus summary works ───────────────────────────
<packageNotFoundError/error/condition>
Error in `library(phyloseq)`: there is no package called 'phyloseq'
Backtrace:
▆
1. └─base::library(phyloseq) at test-ilr.R:11:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.4
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘MicrobeDS’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-prerel-macos-arm64, r-prerel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 1.0.4
Check: installed package size
Result: NOTE
installed size is 55.8Mb
sub-directories of 1Mb or more:
libs 54.2Mb
Flavors: r-prerel-macos-arm64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
attr(,"class")
[1] "gg" "ggplot"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ilr.R:11:3'): clr plus summary works ───────────────────────────
<packageNotFoundError/error/condition>
Error in `library(phyloseq)`: there is no package called 'phyloseq'
Backtrace:
▆
1. └─base::library(phyloseq) at test-ilr.R:11:2
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-arm64
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
attr(,"class")
[1] "gg" "ggplot"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ilr.R:11:3'): clr plus summary works ───────────────────────────
<packageNotFoundError/error/condition>
Error in `library(phyloseq)`: there is no package called 'phyloseq'
Backtrace:
▆
1. └─base::library(phyloseq) at test-ilr.R:11:2
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-x86_64