Aitor Moruno-Cuenca
| Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/singIST |
| git_branch: devel |
| git_last_commit: 8d9d6ba |
| git_last_commit_date: 2026-01-07 04:44:12 -0400 (Wed, 07 Jan 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-14 11:34 -0400 (Sat, 14 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4050 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2028/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singIST 0.99.85 (landing page) Aitor Moruno-Cuenca
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for singIST in R Universe. | ||||||||||||||
|
To the developers/maintainers of the singIST package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singIST.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: singIST |
| Version: 0.99.85 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:singIST.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings singIST_0.99.85.tar.gz |
| StartedAt: 2026-03-14 04:01:52 -0400 (Sat, 14 Mar 2026) |
| EndedAt: 2026-03-14 04:19:52 -0400 (Sat, 14 Mar 2026) |
| EllapsedTime: 1080.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: singIST.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:singIST.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings singIST_0.99.85.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/singIST.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-14 08:01:52 UTC
* checking for file ‘singIST/DESCRIPTION’ ... OK
* this is package ‘singIST’ version ‘0.99.85’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘singIST’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘singIST-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: helpers
> ### Title: Update block of predictor matrices in matrixToBlock()
> ### Aliases: helpers update_block get_measure_index get_train_val_sets
> ### quantile_computation evaluate_quantile_combinations
> ### execute_parallel_cv performance_measures compute_final_measures
> ### select_optimal_PLS execute_sequential_cv initialize_results
> ### permute_Y_matrix compute_permutation_stats select_samples
> ### fit_permuted_model evaluate_performance compute_pvalue compute_IC95
> ### jackknife_CIP_GIP subsampling_CIP_GIP generate_null_distributions
> ### permute_X_matrix calculate_pvalues perform_cv
> ### compute_validation_metrics detect_gene_type
> ### retrieve_one2one_orthologs FCtoExpression center_scale get_indices
> ### deflate_prediction
>
> ### ** Examples
>
> measure <- "F1"
> get_measure_index(measure)
[1] 5
> X <- matrix(rnorm(100), nrow = 10, ncol = 10)
> Y <- matrix(sample(0:1, 10, replace = TRUE), ncol = 1)
> result <- get_train_val_sets(X, Y, validation_index = 2)
> str(result)
List of 4
$ E_matrix_validation: num [1, 1:10] 0.184 0.39 0.782 -0.103 -0.253 ...
$ F_matrix_validation: int [1, 1] 1
$ E_matrix_training : num [1:9, 1:10] -0.626 -0.836 1.595 0.33 -0.82 ...
$ F_matrix_training : int [1:9, 1] 1 0 1 1 1 0 0 1 0
> E_train <- matrix(rnorm(100), nrow = 10, ncol = 10)
> F_train <- matrix(sample(0:1, 10, replace = TRUE), ncol = 1)
> E_valid <- matrix(rnorm(10), nrow = 1, ncol = 10)
> F_valid <- matrix(1, nrow = 1, ncol = 1)
> quantile_table <- matrix(runif(2), nrow = 1, ncol = 2)
> quantile_table_CV <- matrix(runif(7), nrow = 1, ncol = 7)
> results_CV_summary_n <- matrix(0, nrow = 1, ncol = 2)
> F_matrix_validation_bind <- matrix(0, nrow = 1, ncol = 2)
> result <- evaluate_quantile_combinations(j=1, E_matrix_training = E_train,
+ F_matrix_training = F_train,
+ E_matrix_validation = E_valid,
+ F_matrix_validation = F_valid,
+ F_matrix_validation_bind =
+ F_matrix_validation_bind,
+ results_CV_summary_n =
+ results_CV_summary_n,
+ quantile_table_CV=quantile_table_CV,
+ i = 1, X.dim = c(5,5),
+ quantile.comb.table =quantile_table,
+ outcome.type = "binary",
+ center = TRUE,
+ scale = TRUE, maxiter = 100,
+ Method = NULL)
> print(result)
$results_CV_summary_n
[,1] [,2]
[1,] 0 0
$F_matrix_validation_bind
[,1] [,2]
[1,] 1 0
> set.seed(123)
> K <- 5
> X <- matrix(rnorm(50), nrow = 5, ncol = 10)
> Y <- matrix(sample(0:1, 5, replace = TRUE), ncol = 1)
> quantile_comb_table <- matrix(runif(10), nrow = 2, ncol = 10)
> results_CV_summary_n <- matrix(0, nrow = 2, ncol = K)
> F_matrix_validation_bind <- matrix(0, nrow = 2, ncol = K)
> # Parallelization options
> library(BiocParallel)
> register(SnowParam(workers = 2, exportglobals = FALSE, progressbar = TRUE),
+ default = TRUE)
> output <- execute_parallel_cv(K, results_CV_summary_n,
+ F_matrix_validation_bind, X, Y, PLS_term = 1,
+ X.dim = c(5,5),
+ quantile.comb.table = quantile_comb_table,
+ outcome.type = "binary",
+ quantile_table_CV = quantile_comb_table,
+ measure = "B_accuracy",
+ expected.measure.increase = 0.005,
+ center = TRUE, scale = TRUE, maxiter = 100,
+ Method = NULL)
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> register(SerialParam(), default = TRUE) # disable parallelization
> str(output)
List of 2
$ results_CV_summary_n : num [1:2, 1:5] 1 1 1 0 0 0 1 1 1 1
$ F_matrix_validation_bind: num [1:2, 1:5] 0 0 1 1 1 1 0 0 1 1
> initialize_results(100, 3)
$RV.YYpermut.values
dimlabP rep.NA..npermut...1.
1 NoPermut NA
2 permut1 NA
3 permut2 NA
4 permut3 NA
5 permut4 NA
6 permut5 NA
7 permut6 NA
8 permut7 NA
9 permut8 NA
10 permut9 NA
11 permut10 NA
12 permut11 NA
13 permut12 NA
14 permut13 NA
15 permut14 NA
16 permut15 NA
17 permut16 NA
18 permut17 NA
19 permut18 NA
20 permut19 NA
21 permut20 NA
22 permut21 NA
23 permut22 NA
24 permut23 NA
25 permut24 NA
26 permut25 NA
27 permut26 NA
28 permut27 NA
29 permut28 NA
30 permut29 NA
31 permut30 NA
32 permut31 NA
33 permut32 NA
34 permut33 NA
35 permut34 NA
36 permut35 NA
37 permut36 NA
38 permut37 NA
39 permut38 NA
40 permut39 NA
41 permut40 NA
42 permut41 NA
43 permut42 NA
44 permut43 NA
45 permut44 NA
46 permut45 NA
47 permut46 NA
48 permut47 NA
49 permut48 NA
50 permut49 NA
51 permut50 NA
52 permut51 NA
53 permut52 NA
54 permut53 NA
55 permut54 NA
56 permut55 NA
57 permut56 NA
58 permut57 NA
59 permut58 NA
60 permut59 NA
61 permut60 NA
62 permut61 NA
63 permut62 NA
64 permut63 NA
65 permut64 NA
66 permut65 NA
67 permut66 NA
68 permut67 NA
69 permut68 NA
70 permut69 NA
71 permut70 NA
72 permut71 NA
73 permut72 NA
74 permut73 NA
75 permut74 NA
76 permut75 NA
77 permut76 NA
78 permut77 NA
79 permut78 NA
80 permut79 NA
81 permut80 NA
82 permut81 NA
83 permut82 NA
84 permut83 NA
85 permut84 NA
86 permut85 NA
87 permut86 NA
88 permut87 NA
89 permut88 NA
90 permut89 NA
91 permut90 NA
92 permut91 NA
93 permut92 NA
94 permut93 NA
95 permut94 NA
96 permut95 NA
97 permut96 NA
98 permut97 NA
99 permut98 NA
100 permut99 NA
101 permut100 NA
$cor.YYpermut.values
dimlabP X1 X2 X3
1 NoPermut NA NA NA
2 permut1 NA NA NA
3 permut2 NA NA NA
4 permut3 NA NA NA
5 permut4 NA NA NA
6 permut5 NA NA NA
7 permut6 NA NA NA
8 permut7 NA NA NA
9 permut8 NA NA NA
10 permut9 NA NA NA
11 permut10 NA NA NA
12 permut11 NA NA NA
13 permut12 NA NA NA
14 permut13 NA NA NA
15 permut14 NA NA NA
16 permut15 NA NA NA
17 permut16 NA NA NA
18 permut17 NA NA NA
19 permut18 NA NA NA
20 permut19 NA NA NA
21 permut20 NA NA NA
22 permut21 NA NA NA
23 permut22 NA NA NA
24 permut23 NA NA NA
25 permut24 NA NA NA
26 permut25 NA NA NA
27 permut26 NA NA NA
28 permut27 NA NA NA
29 permut28 NA NA NA
30 permut29 NA NA NA
31 permut30 NA NA NA
32 permut31 NA NA NA
33 permut32 NA NA NA
34 permut33 NA NA NA
35 permut34 NA NA NA
36 permut35 NA NA NA
37 permut36 NA NA NA
38 permut37 NA NA NA
39 permut38 NA NA NA
40 permut39 NA NA NA
41 permut40 NA NA NA
42 permut41 NA NA NA
43 permut42 NA NA NA
44 permut43 NA NA NA
45 permut44 NA NA NA
46 permut45 NA NA NA
47 permut46 NA NA NA
48 permut47 NA NA NA
49 permut48 NA NA NA
50 permut49 NA NA NA
51 permut50 NA NA NA
52 permut51 NA NA NA
53 permut52 NA NA NA
54 permut53 NA NA NA
55 permut54 NA NA NA
56 permut55 NA NA NA
57 permut56 NA NA NA
58 permut57 NA NA NA
59 permut58 NA NA NA
60 permut59 NA NA NA
61 permut60 NA NA NA
62 permut61 NA NA NA
63 permut62 NA NA NA
64 permut63 NA NA NA
65 permut64 NA NA NA
66 permut65 NA NA NA
67 permut66 NA NA NA
68 permut67 NA NA NA
69 permut68 NA NA NA
70 permut69 NA NA NA
71 permut70 NA NA NA
72 permut71 NA NA NA
73 permut72 NA NA NA
74 permut73 NA NA NA
75 permut74 NA NA NA
76 permut75 NA NA NA
77 permut76 NA NA NA
78 permut77 NA NA NA
79 permut78 NA NA NA
80 permut79 NA NA NA
81 permut80 NA NA NA
82 permut81 NA NA NA
83 permut82 NA NA NA
84 permut83 NA NA NA
85 permut84 NA NA NA
86 permut85 NA NA NA
87 permut86 NA NA NA
88 permut87 NA NA NA
89 permut88 NA NA NA
90 permut89 NA NA NA
91 permut90 NA NA NA
92 permut91 NA NA NA
93 permut92 NA NA NA
94 permut93 NA NA NA
95 permut94 NA NA NA
96 permut95 NA NA NA
97 permut96 NA NA NA
98 permut97 NA NA NA
99 permut98 NA NA NA
100 permut99 NA NA NA
101 permut100 NA NA NA
$prctGlob.Ychange.values
dimlabP rep.NA..npermut...1.
1 NoPermut NA
2 permut1 NA
3 permut2 NA
4 permut3 NA
5 permut4 NA
6 permut5 NA
7 permut6 NA
8 permut7 NA
9 permut8 NA
10 permut9 NA
11 permut10 NA
12 permut11 NA
13 permut12 NA
14 permut13 NA
15 permut14 NA
16 permut15 NA
17 permut16 NA
18 permut17 NA
19 permut18 NA
20 permut19 NA
21 permut20 NA
22 permut21 NA
23 permut22 NA
24 permut23 NA
25 permut24 NA
26 permut25 NA
27 permut26 NA
28 permut27 NA
29 permut28 NA
30 permut29 NA
31 permut30 NA
32 permut31 NA
33 permut32 NA
34 permut33 NA
35 permut34 NA
36 permut35 NA
37 permut36 NA
38 permut37 NA
39 permut38 NA
40 permut39 NA
41 permut40 NA
42 permut41 NA
43 permut42 NA
44 permut43 NA
45 permut44 NA
46 permut45 NA
47 permut46 NA
48 permut47 NA
49 permut48 NA
50 permut49 NA
51 permut50 NA
52 permut51 NA
53 permut52 NA
54 permut53 NA
55 permut54 NA
56 permut55 NA
57 permut56 NA
58 permut57 NA
59 permut58 NA
60 permut59 NA
61 permut60 NA
62 permut61 NA
63 permut62 NA
64 permut63 NA
65 permut64 NA
66 permut65 NA
67 permut66 NA
68 permut67 NA
69 permut68 NA
70 permut69 NA
71 permut70 NA
72 permut71 NA
73 permut72 NA
74 permut73 NA
75 permut74 NA
76 permut75 NA
77 permut76 NA
78 permut77 NA
79 permut78 NA
80 permut79 NA
81 permut80 NA
82 permut81 NA
83 permut82 NA
84 permut83 NA
85 permut84 NA
86 permut85 NA
87 permut86 NA
88 permut87 NA
89 permut88 NA
90 permut89 NA
91 permut90 NA
92 permut91 NA
93 permut92 NA
94 permut93 NA
95 permut94 NA
96 permut95 NA
97 permut96 NA
98 permut97 NA
99 permut98 NA
100 permut99 NA
101 permut100 NA
$prct.Ychange.values
dimlabP X1 X2 X3 X4
1 NoPermut NA NA NA NA
2 permut1 NA NA NA NA
3 permut2 NA NA NA NA
4 permut3 NA NA NA NA
5 permut4 NA NA NA NA
6 permut5 NA NA NA NA
7 permut6 NA NA NA NA
8 permut7 NA NA NA NA
9 permut8 NA NA NA NA
10 permut9 NA NA NA NA
11 permut10 NA NA NA NA
12 permut11 NA NA NA NA
13 permut12 NA NA NA NA
14 permut13 NA NA NA NA
15 permut14 NA NA NA NA
16 permut15 NA NA NA NA
17 permut16 NA NA NA NA
18 permut17 NA NA NA NA
19 permut18 NA NA NA NA
20 permut19 NA NA NA NA
21 permut20 NA NA NA NA
22 permut21 NA NA NA NA
23 permut22 NA NA NA NA
24 permut23 NA NA NA NA
25 permut24 NA NA NA NA
26 permut25 NA NA NA NA
27 permut26 NA NA NA NA
28 permut27 NA NA NA NA
29 permut28 NA NA NA NA
30 permut29 NA NA NA NA
31 permut30 NA NA NA NA
32 permut31 NA NA NA NA
33 permut32 NA NA NA NA
34 permut33 NA NA NA NA
35 permut34 NA NA NA NA
36 permut35 NA NA NA NA
37 permut36 NA NA NA NA
38 permut37 NA NA NA NA
39 permut38 NA NA NA NA
40 permut39 NA NA NA NA
41 permut40 NA NA NA NA
42 permut41 NA NA NA NA
43 permut42 NA NA NA NA
44 permut43 NA NA NA NA
45 permut44 NA NA NA NA
46 permut45 NA NA NA NA
47 permut46 NA NA NA NA
48 permut47 NA NA NA NA
49 permut48 NA NA NA NA
50 permut49 NA NA NA NA
51 permut50 NA NA NA NA
52 permut51 NA NA NA NA
53 permut52 NA NA NA NA
54 permut53 NA NA NA NA
55 permut54 NA NA NA NA
56 permut55 NA NA NA NA
57 permut56 NA NA NA NA
58 permut57 NA NA NA NA
59 permut58 NA NA NA NA
60 permut59 NA NA NA NA
61 permut60 NA NA NA NA
62 permut61 NA NA NA NA
63 permut62 NA NA NA NA
64 permut63 NA NA NA NA
65 permut64 NA NA NA NA
66 permut65 NA NA NA NA
67 permut66 NA NA NA NA
68 permut67 NA NA NA NA
69 permut68 NA NA NA NA
70 permut69 NA NA NA NA
71 permut70 NA NA NA NA
72 permut71 NA NA NA NA
73 permut72 NA NA NA NA
74 permut73 NA NA NA NA
75 permut74 NA NA NA NA
76 permut75 NA NA NA NA
77 permut76 NA NA NA NA
78 permut77 NA NA NA NA
79 permut78 NA NA NA NA
80 permut79 NA NA NA NA
81 permut80 NA NA NA NA
82 permut81 NA NA NA NA
83 permut82 NA NA NA NA
84 permut83 NA NA NA NA
85 permut84 NA NA NA NA
86 permut85 NA NA NA NA
87 permut86 NA NA NA NA
88 permut87 NA NA NA NA
89 permut88 NA NA NA NA
90 permut89 NA NA NA NA
91 permut90 NA NA NA NA
92 permut91 NA NA NA NA
93 permut92 NA NA NA NA
94 permut93 NA NA NA NA
95 permut94 NA NA NA NA
96 permut95 NA NA NA NA
97 permut96 NA NA NA NA
98 permut97 NA NA NA NA
99 permut98 NA NA NA NA
100 permut99 NA NA NA NA
101 permut100 NA NA NA NA
> permute_Y_matrix(matrix(rnorm(100), 10, 10), nr = 10, nbObsPermut = 3, j = 2)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.7729782 -0.900791751 -0.31939381 -0.62795166 0.03768285 0.4856014
[2,] 2.1499193 -0.735026156 0.08454377 -0.04691673 1.17622012 -0.2657389
[3,] 0.4958705 0.619283535 -0.62591091 1.29230591 -0.94561794 1.3766098
[4,] -0.1524106 -0.778997240 0.20637270 0.18367824 1.39742665 0.8538955
[5,] 1.2339762 -0.006198262 -0.90087086 -0.46355650 -0.66518864 -0.1803943
[6,] 0.6343621 -0.685706846 0.66372867 0.30546323 0.45203019 -1.5676751
[7,] -1.3343536 -1.427685784 -0.76847360 0.16261812 -0.55853581 0.1516114
[8,] 0.7935853 -0.782730275 0.07485682 0.41036345 -0.23026224 0.9618104
[9,] 0.4120223 -0.279333528 0.30027912 -0.08398871 0.52685567 -0.2607259
[10,] -0.2288958 -0.374800093 -0.48892284 1.77874162 1.76365303 0.4187967
[,7] [,8] [,9] [,10]
[1,] 0.3399565 1.646474838 -0.7554640 0.61097114
[2,] 0.5964251 0.192996186 -0.2639929 -0.04786774
[3,] 0.6028704 0.007051323 0.4406921 -0.01931896
[4,] 1.1174865 0.382131608 0.8374551 1.06643034
[5,] -0.7661688 -2.494835444 -1.2774508 -0.08868545
[6,] -0.6203265 -0.977296362 1.1771920 -1.59548490
[7,] 1.8714180 -0.392553554 -0.7524627 -2.39919771
[8,] -0.2419765 -0.084140473 -1.2613042 -0.71356081
[9,] 0.7901903 0.628568823 0.9025058 0.85170932
[10,] 1.1849306 -1.093413799 -2.3482903 -0.53624259
> res <- initialize_results(100, 3)
> compute_permutation_stats(res, matrix(rnorm(100), 10, 10),
+ matrix(rnorm(100), 10, 10), j = 2, q = 3, nr = 10)
Warning in matrix(value, n, p) :
data length [10] is not a sub-multiple or multiple of the number of columns [4]
$RV.YYpermut.values
dimlabP rep.NA..npermut...1.
1 NoPermut NA
2 permut1 0.6321216
3 permut2 NA
4 permut3 NA
5 permut4 NA
6 permut5 NA
7 permut6 NA
8 permut7 NA
9 permut8 NA
10 permut9 NA
11 permut10 NA
12 permut11 NA
13 permut12 NA
14 permut13 NA
15 permut14 NA
16 permut15 NA
17 permut16 NA
18 permut17 NA
19 permut18 NA
20 permut19 NA
21 permut20 NA
22 permut21 NA
23 permut22 NA
24 permut23 NA
25 permut24 NA
26 permut25 NA
27 permut26 NA
28 permut27 NA
29 permut28 NA
30 permut29 NA
31 permut30 NA
32 permut31 NA
33 permut32 NA
34 permut33 NA
35 permut34 NA
36 permut35 NA
37 permut36 NA
38 permut37 NA
39 permut38 NA
40 permut39 NA
41 permut40 NA
42 permut41 NA
43 permut42 NA
44 permut43 NA
45 permut44 NA
46 permut45 NA
47 permut46 NA
48 permut47 NA
49 permut48 NA
50 permut49 NA
51 permut50 NA
52 permut51 NA
53 permut52 NA
54 permut53 NA
55 permut54 NA
56 permut55 NA
57 permut56 NA
58 permut57 NA
59 permut58 NA
60 permut59 NA
61 permut60 NA
62 permut61 NA
63 permut62 NA
64 permut63 NA
65 permut64 NA
66 permut65 NA
67 permut66 NA
68 permut67 NA
69 permut68 NA
70 permut69 NA
71 permut70 NA
72 permut71 NA
73 permut72 NA
74 permut73 NA
75 permut74 NA
76 permut75 NA
77 permut76 NA
78 permut77 NA
79 permut78 NA
80 permut79 NA
81 permut80 NA
82 permut81 NA
83 permut82 NA
84 permut83 NA
85 permut84 NA
86 permut85 NA
87 permut86 NA
88 permut87 NA
89 permut88 NA
90 permut89 NA
91 permut90 NA
92 permut91 NA
93 permut92 NA
94 permut93 NA
95 permut94 NA
96 permut95 NA
97 permut96 NA
98 permut97 NA
99 permut98 NA
100 permut99 NA
101 permut100 NA
$cor.YYpermut.values
dimlabP X1 X2 X3
1 NoPermut NA NA NA
2 permut1 0.3202317 -0.4912541 -0.09637866
3 permut2 NA NA NA
4 permut3 NA NA NA
5 permut4 NA NA NA
6 permut5 NA NA NA
7 permut6 NA NA NA
8 permut7 NA NA NA
9 permut8 NA NA NA
10 permut9 NA NA NA
11 permut10 NA NA NA
12 permut11 NA NA NA
13 permut12 NA NA NA
14 permut13 NA NA NA
15 permut14 NA NA NA
16 permut15 NA NA NA
17 permut16 NA NA NA
18 permut17 NA NA NA
19 permut18 NA NA NA
20 permut19 NA NA NA
21 permut20 NA NA NA
22 permut21 NA NA NA
23 permut22 NA NA NA
24 permut23 NA NA NA
25 permut24 NA NA NA
26 permut25 NA NA NA
27 permut26 NA NA NA
28 permut27 NA NA NA
29 permut28 NA NA NA
30 permut29 NA NA NA
31 permut30 NA NA NA
32 permut31 NA NA NA
33 permut32 NA NA NA
34 permut33 NA NA NA
35 permut34 NA NA NA
36 permut35 NA NA NA
37 permut36 NA NA NA
38 permut37 NA NA NA
39 permut38 NA NA NA
40 permut39 NA NA NA
41 permut40 NA NA NA
42 permut41 NA NA NA
43 permut42 NA NA NA
44 permut43 NA NA NA
45 permut44 NA NA NA
46 permut45 NA NA NA
47 permut46 NA NA NA
48 permut47 NA NA NA
49 permut48 NA NA NA
50 permut49 NA NA NA
51 permut50 NA NA NA
52 permut51 NA NA NA
53 permut52 NA NA NA
54 permut53 NA NA NA
55 permut54 NA NA NA
56 permut55 NA NA NA
57 permut56 NA NA NA
58 permut57 NA NA NA
59 permut58 NA NA NA
60 permut59 NA NA NA
61 permut60 NA NA NA
62 permut61 NA NA NA
63 permut62 NA NA NA
64 permut63 NA NA NA
65 permut64 NA NA NA
66 permut65 NA NA NA
67 permut66 NA NA NA
68 permut67 NA NA NA
69 permut68 NA NA NA
70 permut69 NA NA NA
71 permut70 NA NA NA
72 permut71 NA NA NA
73 permut72 NA NA NA
74 permut73 NA NA NA
75 permut74 NA NA NA
76 permut75 NA NA NA
77 permut76 NA NA NA
78 permut77 NA NA NA
79 permut78 NA NA NA
80 permut79 NA NA NA
81 permut80 NA NA NA
82 permut81 NA NA NA
83 permut82 NA NA NA
84 permut83 NA NA NA
85 permut84 NA NA NA
86 permut85 NA NA NA
87 permut86 NA NA NA
88 permut87 NA NA NA
89 permut88 NA NA NA
90 permut89 NA NA NA
91 permut90 NA NA NA
92 permut91 NA NA NA
93 permut92 NA NA NA
94 permut93 NA NA NA
95 permut94 NA NA NA
96 permut95 NA NA NA
97 permut96 NA NA NA
98 permut97 NA NA NA
99 permut98 NA NA NA
100 permut99 NA NA NA
101 permut100 NA NA NA
$prctGlob.Ychange.values
dimlabP rep.NA..npermut...1.
1 NoPermut NA
2 permut1 2.327239
3 permut2 NA
4 permut3 NA
5 permut4 NA
6 permut5 NA
7 permut6 NA
8 permut7 NA
9 permut8 NA
10 permut9 NA
11 permut10 NA
12 permut11 NA
13 permut12 NA
14 permut13 NA
15 permut14 NA
16 permut15 NA
17 permut16 NA
18 permut17 NA
19 permut18 NA
20 permut19 NA
21 permut20 NA
22 permut21 NA
23 permut22 NA
24 permut23 NA
25 permut24 NA
26 permut25 NA
27 permut26 NA
28 permut27 NA
29 permut28 NA
30 permut29 NA
31 permut30 NA
32 permut31 NA
33 permut32 NA
34 permut33 NA
35 permut34 NA
36 permut35 NA
37 permut36 NA
38 permut37 NA
39 permut38 NA
40 permut39 NA
41 permut40 NA
42 permut41 NA
43 permut42 NA
44 permut43 NA
45 permut44 NA
46 permut45 NA
47 permut46 NA
48 permut47 NA
49 permut48 NA
50 permut49 NA
51 permut50 NA
52 permut51 NA
53 permut52 NA
54 permut53 NA
55 permut54 NA
56 permut55 NA
57 permut56 NA
58 permut57 NA
59 permut58 NA
60 permut59 NA
61 permut60 NA
62 permut61 NA
63 permut62 NA
64 permut63 NA
65 permut64 NA
66 permut65 NA
67 permut66 NA
68 permut67 NA
69 permut68 NA
70 permut69 NA
71 permut70 NA
72 permut71 NA
73 permut72 NA
74 permut73 NA
75 permut74 NA
76 permut75 NA
77 permut76 NA
78 permut77 NA
79 permut78 NA
80 permut79 NA
81 permut80 NA
82 permut81 NA
83 permut82 NA
84 permut83 NA
85 permut84 NA
86 permut85 NA
87 permut86 NA
88 permut87 NA
89 permut88 NA
90 permut89 NA
91 permut90 NA
92 permut91 NA
93 permut92 NA
94 permut93 NA
95 permut94 NA
96 permut95 NA
97 permut96 NA
98 permut97 NA
99 permut98 NA
100 permut99 NA
101 permut100 NA
$prct.Ychange.values
dimlabP X1 X2 X3 X4
1 NoPermut NA NA NA NA
2 permut1 1 1 1 1
3 permut2 NA NA NA NA
4 permut3 NA NA NA NA
5 permut4 NA NA NA NA
6 permut5 NA NA NA NA
7 permut6 NA NA NA NA
8 permut7 NA NA NA NA
9 permut8 NA NA NA NA
10 permut9 NA NA NA NA
11 permut10 NA NA NA NA
12 permut11 NA NA NA NA
13 permut12 NA NA NA NA
14 permut13 NA NA NA NA
15 permut14 NA NA NA NA
16 permut15 NA NA NA NA
17 permut16 NA NA NA NA
18 permut17 NA NA NA NA
19 permut18 NA NA NA NA
20 permut19 NA NA NA NA
21 permut20 NA NA NA NA
22 permut21 NA NA NA NA
23 permut22 NA NA NA NA
24 permut23 NA NA NA NA
25 permut24 NA NA NA NA
26 permut25 NA NA NA NA
27 permut26 NA NA NA NA
28 permut27 NA NA NA NA
29 permut28 NA NA NA NA
30 permut29 NA NA NA NA
31 permut30 NA NA NA NA
32 permut31 NA NA NA NA
33 permut32 NA NA NA NA
34 permut33 NA NA NA NA
35 permut34 NA NA NA NA
36 permut35 NA NA NA NA
37 permut36 NA NA NA NA
38 permut37 NA NA NA NA
39 permut38 NA NA NA NA
40 permut39 NA NA NA NA
41 permut40 NA NA NA NA
42 permut41 NA NA NA NA
43 permut42 NA NA NA NA
44 permut43 NA NA NA NA
45 permut44 NA NA NA NA
46 permut45 NA NA NA NA
47 permut46 NA NA NA NA
48 permut47 NA NA NA NA
49 permut48 NA NA NA NA
50 permut49 NA NA NA NA
51 permut50 NA NA NA NA
52 permut51 NA NA NA NA
53 permut52 NA NA NA NA
54 permut53 NA NA NA NA
55 permut54 NA NA NA NA
56 permut55 NA NA NA NA
57 permut56 NA NA NA NA
58 permut57 NA NA NA NA
59 permut58 NA NA NA NA
60 permut59 NA NA NA NA
61 permut60 NA NA NA NA
62 permut61 NA NA NA NA
63 permut62 NA NA NA NA
64 permut63 NA NA NA NA
65 permut64 NA NA NA NA
66 permut65 NA NA NA NA
67 permut66 NA NA NA NA
68 permut67 NA NA NA NA
69 permut68 NA NA NA NA
70 permut69 NA NA NA NA
71 permut70 NA NA NA NA
72 permut71 NA NA NA NA
73 permut72 NA NA NA NA
74 permut73 NA NA NA NA
75 permut74 NA NA NA NA
76 permut75 NA NA NA NA
77 permut76 NA NA NA NA
78 permut77 NA NA NA NA
79 permut78 NA NA NA NA
80 permut79 NA NA NA NA
81 permut80 NA NA NA NA
82 permut81 NA NA NA NA
83 permut82 NA NA NA NA
84 permut83 NA NA NA NA
85 permut84 NA NA NA NA
86 permut85 NA NA NA NA
87 permut86 NA NA NA NA
88 permut87 NA NA NA NA
89 permut88 NA NA NA NA
90 permut89 NA NA NA NA
91 permut90 NA NA NA NA
92 permut91 NA NA NA NA
93 permut92 NA NA NA NA
94 permut93 NA NA NA NA
95 permut94 NA NA NA NA
96 permut95 NA NA NA NA
97 permut96 NA NA NA NA
98 permut97 NA NA NA NA
99 permut98 NA NA NA NA
100 permut99 NA NA NA NA
101 permut100 NA NA NA NA
> null_errors <- c(0.3, 0.4, 0.35, 0.33)
> CV_error <- 0.32
> compute_pvalue(null_errors, CV_error)
[1] 0.75
> null_errors <- c(0.3, 0.4, 0.35, 0.33)
> compute_IC95(null_errors)
5% 95%
0.3045 0.3925
> library(biomaRt)
> gene_set <- c("IL13", "IL4", "IL5", "IL21")
> mart <- biomaRt::useMart(biomart = "ensembl",
+ dataset = "hsapiens_gene_ensembl")
Error: Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.23-bioc/meat/singIST.Rcheck/00check.log’
for details.
singIST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL singIST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘singIST’ ... ** this is package ‘singIST’ version ‘0.99.85’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (singIST)
singIST.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(singIST)
>
> test_check("singIST")
[ FAIL 0 | WARN 0 | SKIP 25 | PASS 12 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-CIP_GIP.R:2:5', 'test-asmbPLSDAcvloo.R:2:5',
'test-biological_link_function.R:2:5', 'test-celltype_mapping.R:2:5',
'test-celltype_recap.R:2:5', 'test-derive_contributions.R:2:5',
'test-derive_scores.R:2:5', 'test-diff_expressed.R:2:5',
'test-gene_contrib.R:2:5', 'test-hyperparameters.R:2:5',
'test-mappingorganism.R:2:5', 'test-matrixToBlock.R:2:5',
'test-multiple_check.R:2:5', 'test-multiple_fitOptimal.R:2:5',
'test-multiple_singISTrecapitulations.R:2:5', 'test-orthology_mapping.R:2:5',
'test-pathway.R:2:5', 'test-permut_asmbplsda.R:2:5',
'test-setGeneSetsCelltype.R:2:5', 'test-singIST_treat.R:2:5',
'test-singISTrecapitulations.R:2:5', 'test-superpathway_recap.R:2:5',
'test-superpathwayfitmodel.R:2:5', 'test-superpathwayinput.R:2:5',
'test-wilcox_CIP_GIP.R:2:5'
[ FAIL 0 | WARN 0 | SKIP 25 | PASS 12 ]
>
> proc.time()
user system elapsed
18.772 1.202 19.963
singIST.Rcheck/singIST-Ex.timings
| name | user | system | elapsed | |
| CIP_GIP | 0.023 | 0.007 | 0.029 | |
| CIP_GIP_test | 0.131 | 0.059 | 0.190 | |
| Results_comparison_measure | 0 | 0 | 0 | |
| asmbPLSDA.cv.kcv | 0.130 | 0.024 | 0.155 | |
| asmbPLSDA.cv.loo | 3.795 | 0.223 | 3.987 | |
| biological_link_function | 0.053 | 0.062 | 0.027 | |
| celltype_mapping | 0.066 | 0.007 | 0.073 | |
| celltype_recap | 0.022 | 0.000 | 0.022 | |
| check_hyperparameters | 0.055 | 0.021 | 0.071 | |
| check_mapping_organism | 0.003 | 0.000 | 0.003 | |
| check_pathway | 0 | 0 | 0 | |
| check_superpathway | 0 | 0 | 0 | |
| check_superpathway_input | 0.002 | 0.001 | 0.003 | |
| clean_mfa_data | 0.001 | 0.001 | 0.002 | |
| create_fit_model | 0.002 | 0.001 | 0.003 | |
| create_hyperparameters | 0.000 | 0.001 | 0.001 | |
| create_mapping_organism | 0.000 | 0.001 | 0.001 | |
| create_pathway | 0.000 | 0.001 | 0.001 | |
| create_superpathway | 0.001 | 0.000 | 0.001 | |
| create_superpathway_input | 0.001 | 0.001 | 0.002 | |
| derive_contributions | 0.022 | 0.000 | 0.022 | |
| derive_scores | 0.020 | 0.002 | 0.022 | |
| diff_expressed | 0.569 | 0.054 | 0.623 | |
| fitOptimal | 0.822 | 0.279 | 1.101 | |
| fit_mfa_imputer | 0.038 | 0.000 | 0.038 | |
| gene_contrib | 0.021 | 0.001 | 0.022 | |