Christian Mertes
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: RELEASE_3_21 |
| git_last_commit: 174dc26 |
| git_last_commit_date: 2025-07-28 15:29:40 -0400 (Mon, 28 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1512/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.26.3 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OUTRIDER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OUTRIDER.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OUTRIDER |
| Version: 1.26.3 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OUTRIDER_1.26.3.tar.gz |
| StartedAt: 2025-10-14 12:16:37 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 12:26:37 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 600.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OUTRIDER_1.26.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.26.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘OUTRIDER’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'ggbio:::.buildFacetsFromArgs'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'checkOutriderDataSet'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estimateBestQ: no visible binding for global variable ‘oht’
plotEncDimSearch.OUTRIDER: no visible binding for global variable ‘oht’
plotEncDimSearch.OUTRIDER: no visible binding for global variable
‘singular_values’
plotEncDimSearch,OutriderDataSet: no visible binding for global
variable ‘oht’
plotEncDimSearch,OutriderDataSet: no visible binding for global
variable ‘singular_values’
Undefined global functions or variables:
oht singular_values
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'getter_setter_functions.Rd':
‘[DESeq2]{estimateDispersions}’
Non-topic package-anchored link(s) in Rd file 'sizeFactors.Rd':
‘[DESeq2]{estimateSizeFactors}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OUTRIDER-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OUTRIDER
> ### Title: OUTRIDER - Finding expression outlier events
> ### Aliases: OUTRIDER
>
> ### ** Examples
>
> ods <- makeExampleOutriderDataSet()
> implementation <- 'autoencoder'
> ## Don't show:
> ods <- ods[1:10,1:10]
> implementation <- 'pca'
> ## End(Don't show)
> ods <- OUTRIDER(ods, implementation=implementation)
Tue Oct 14 12:24:39 2025: SizeFactor estimation ...
Tue Oct 14 12:24:39 2025: Controlling for confounders ...
Using provided q with: 10
Tue Oct 14 12:24:39 2025: Using the pca implementation for controlling.
Tue Oct 14 12:24:40 2025: Used the pca implementation for controlling.
Tue Oct 14 12:24:40 2025: Fitting the data ...
Tue Oct 14 12:24:44 2025: P-value calculation ...
Tue Oct 14 12:24:45 2025: Zscore calculation ...
>
> pValue(ods)[1:10,1:10]
sample_1 sample_2 sample_3 sample_4 sample_5 sample_6
feature_1 0.9708112 0.9673898 1.0000000 1.0000000 0.9682199 0.9715971
feature_2 1.0000000 0.9645359 0.9956326 0.9691272 0.9565509 1.0000000
feature_3 0.9956214 1.0000000 0.9817906 0.9714409 0.9874758 1.0000000
feature_4 0.9172160 1.0000000 0.8531784 0.9520697 0.9681790 0.9964730
feature_5 0.9341059 0.9465044 0.8974455 0.9659065 1.0000000 1.0000000
feature_6 0.9589618 0.9899073 0.8672567 1.0000000 1.0000000 0.8466523
feature_7 0.9996636 0.9941701 0.9987946 0.9951733 0.9949322 0.9736942
feature_8 1.0000000 0.9589015 0.8852728 1.0000000 0.9101463 0.8960677
feature_9 0.9944175 0.9819508 0.9432241 1.0000000 0.9670230 1.0000000
feature_10 1.0000000 0.9713634 1.0000000 0.9862026 0.9942747 0.9858947
sample_7 sample_8 sample_9 sample_10
feature_1 0.9654920 1.0000000 0.9479204 0.9599123
feature_2 1.0000000 0.9600617 0.9691272 0.9950102
feature_3 0.9944387 0.9835739 1.0000000 1.0000000
feature_4 0.9738876 0.9834010 0.9285130 0.9901875
feature_5 0.9985055 1.0000000 0.9314466 1.0000000
feature_6 0.9361394 0.9962628 0.9703490 0.9706844
feature_7 1.0000000 1.0000000 0.9939868 0.9878672
feature_8 0.9879651 0.9976097 0.9930988 0.9906877
feature_9 1.0000000 0.9898412 0.9810968 1.0000000
feature_10 0.9773213 0.9988272 1.0000000 1.0000000
> res <- results(ods, all=TRUE)
> res
Key: <geneID, sampleID>
geneID sampleID pValue padjust zScore l2fc rawcounts
<char> <char> <num> <num> <num> <num> <int>
1: feature_1 sample_1 0.9708112 1 -0.26 -0.02 58
2: feature_1 sample_10 0.9599123 1 -0.99 -0.04 35
3: feature_1 sample_2 0.9673898 1 -0.46 -0.03 49
4: feature_1 sample_3 1.0000000 1 0.74 0.00 434
5: feature_1 sample_4 1.0000000 1 0.83 0.00 1052
6: feature_1 sample_5 0.9682199 1 -0.41 -0.03 51
7: feature_1 sample_6 0.9715971 1 0.88 0.00 4121
8: feature_1 sample_7 0.9654920 1 0.89 0.00 5031
9: feature_1 sample_8 1.0000000 1 0.80 0.00 691
10: feature_1 sample_9 0.9479204 1 -2.03 -0.06 22
11: feature_10 sample_1 1.0000000 1 0.54 0.00 1449
12: feature_10 sample_10 1.0000000 1 0.66 0.00 2818
13: feature_10 sample_2 0.9713634 1 0.77 0.00 27702
14: feature_10 sample_3 1.0000000 1 0.57 0.00 1673
15: feature_10 sample_4 0.9862026 1 -0.71 -0.01 238
16: feature_10 sample_5 0.9942747 1 0.17 0.00 580
17: feature_10 sample_6 0.9858947 1 -0.75 -0.01 231
18: feature_10 sample_7 0.9773213 1 -2.37 -0.01 112
19: feature_10 sample_8 0.9988272 1 0.44 0.00 1036
20: feature_10 sample_9 1.0000000 1 0.67 0.00 2984
21: feature_2 sample_1 1.0000000 1 0.76 0.00 1033
22: feature_2 sample_10 0.9950102 1 0.50 -0.01 241
23: feature_2 sample_2 0.9645359 1 -1.10 -0.03 42
24: feature_2 sample_3 0.9956326 1 0.79 0.00 1592
25: feature_2 sample_4 0.9691272 1 -0.74 -0.03 52
26: feature_2 sample_5 0.9565509 1 -1.84 -0.05 30
27: feature_2 sample_6 1.0000000 1 0.78 0.00 1247
28: feature_2 sample_7 1.0000000 1 0.76 0.00 1041
29: feature_2 sample_8 0.9600617 1 0.83 0.00 5113
30: feature_2 sample_9 0.9691272 1 -0.74 -0.03 52
31: feature_3 sample_1 0.9956214 1 -0.04 0.00 404
32: feature_3 sample_10 1.0000000 1 0.59 0.00 1238
33: feature_3 sample_2 1.0000000 1 0.67 0.00 1690
34: feature_3 sample_3 0.9817906 1 -1.96 -0.01 130
35: feature_3 sample_4 0.9714409 1 0.84 0.00 8658
36: feature_3 sample_5 0.9874758 1 0.80 0.00 4329
37: feature_3 sample_6 1.0000000 1 0.32 0.00 657
38: feature_3 sample_7 0.9944387 1 -0.14 0.00 363
39: feature_3 sample_8 0.9835739 1 -1.62 -0.01 148
40: feature_3 sample_9 1.0000000 1 0.54 0.00 1062
41: feature_4 sample_1 0.9172160 1 -0.67 -0.17 7
42: feature_4 sample_10 0.9901875 1 0.39 -0.03 48
43: feature_4 sample_2 1.0000000 1 0.57 -0.01 235
44: feature_4 sample_3 0.8531784 1 -2.53 -0.42 2
45: feature_4 sample_4 0.9520697 1 0.59 0.00 541
46: feature_4 sample_5 0.9681790 1 0.59 0.00 427
47: feature_4 sample_6 0.9964730 1 0.57 -0.01 278
48: feature_4 sample_7 0.9738876 1 0.58 0.00 392
49: feature_4 sample_8 0.9834010 1 0.34 -0.04 39
50: feature_4 sample_9 0.9285130 1 -0.43 -0.14 9
51: feature_5 sample_1 0.9341059 1 0.88 0.00 336
52: feature_5 sample_10 1.0000000 1 0.73 -0.01 120
53: feature_5 sample_2 0.9465044 1 -1.33 -0.12 11
54: feature_5 sample_3 0.8974455 1 0.91 0.00 497
55: feature_5 sample_4 0.9659065 1 -0.58 -0.08 17
56: feature_5 sample_5 1.0000000 1 0.29 -0.03 41
57: feature_5 sample_6 1.0000000 1 0.45 -0.03 54
58: feature_5 sample_7 0.9985055 1 0.22 -0.04 37
59: feature_5 sample_8 1.0000000 1 0.47 -0.03 56
60: feature_5 sample_9 0.9314466 1 -2.05 -0.15 8
61: feature_6 sample_1 0.9589618 1 0.35 -0.04 39
62: feature_6 sample_10 0.9706844 1 0.45 -0.02 74
63: feature_6 sample_2 0.9899073 1 0.56 0.00 398
64: feature_6 sample_3 0.8672567 1 -1.54 -0.32 3
65: feature_6 sample_4 1.0000000 1 0.58 0.00 2050
66: feature_6 sample_5 1.0000000 1 0.58 0.00 2075
67: feature_6 sample_6 0.8466523 1 -2.16 -0.42 2
68: feature_6 sample_7 0.9361394 1 0.04 -0.08 16
69: feature_6 sample_8 0.9962628 1 0.57 0.00 939
70: feature_6 sample_9 0.9703490 1 0.58 0.00 59866
71: feature_7 sample_1 0.9996636 1 0.27 0.00 1095
72: feature_7 sample_10 0.9878672 1 -2.29 -0.01 275
73: feature_7 sample_2 0.9941701 1 0.99 0.00 6690
74: feature_7 sample_3 0.9987946 1 0.16 0.00 980
75: feature_7 sample_4 0.9951733 1 -0.39 0.00 623
76: feature_7 sample_5 0.9949322 1 -0.43 0.00 605
77: feature_7 sample_6 0.9736942 1 1.09 0.00 23938
78: feature_7 sample_7 1.0000000 1 0.67 0.00 2051
79: feature_7 sample_8 1.0000000 1 0.56 0.00 1647
80: feature_7 sample_9 0.9939868 1 -0.62 0.00 540
81: feature_8 sample_1 1.0000000 1 0.56 -0.01 217
82: feature_8 sample_10 0.9906877 1 0.46 -0.02 90
83: feature_8 sample_2 0.9589015 1 0.09 -0.05 26
84: feature_8 sample_3 0.8852728 1 -2.08 -0.26 4
85: feature_8 sample_4 1.0000000 1 0.58 0.00 323
86: feature_8 sample_5 0.9101463 1 0.62 0.00 3174
87: feature_8 sample_6 0.8960677 1 -1.66 -0.22 5
88: feature_8 sample_7 0.9879651 1 0.44 -0.02 80
89: feature_8 sample_8 0.9976097 1 0.51 -0.01 122
90: feature_8 sample_9 0.9930988 1 0.48 -0.01 100
91: feature_9 sample_1 0.9944175 1 0.34 0.00 503
92: feature_9 sample_10 1.0000000 1 0.45 0.00 2206
93: feature_9 sample_2 0.9819508 1 0.02 -0.01 152
94: feature_9 sample_3 0.9432241 1 -2.80 -0.07 20
95: feature_9 sample_4 1.0000000 1 0.44 0.00 1830
96: feature_9 sample_5 0.9670230 1 0.47 0.00 22553
97: feature_9 sample_6 1.0000000 1 0.41 0.00 1030
98: feature_9 sample_7 1.0000000 1 0.44 0.00 1934
99: feature_9 sample_8 0.9898412 1 0.25 0.00 310
100: feature_9 sample_9 0.9810968 1 -0.01 -0.01 142
geneID sampleID pValue padjust zScore l2fc rawcounts
meanRawcounts normcounts meanCorrected theta aberrant AberrantBySample
<num> <num> <num> <num> <lgcl> <num>
1: 1154.4 242.52 243.43 120191.17 FALSE 0
2: 1154.4 239.85 243.43 120191.17 FALSE 0
3: 1154.4 241.77 243.43 120191.17 FALSE 0
4: 1154.4 246.13 243.43 120191.17 FALSE 0
5: 1154.4 246.47 243.43 120191.17 FALSE 0
6: 1154.4 241.96 243.43 120191.17 FALSE 0
7: 1154.4 246.64 243.43 120191.17 FALSE 0
8: 1154.4 246.65 243.43 120191.17 FALSE 0
9: 1154.4 246.35 243.43 120191.17 FALSE 0
10: 1154.4 235.98 243.43 120191.17 FALSE 0
11: 3882.3 1078.11 1076.47 244289.23 FALSE 0
12: 3882.3 1078.47 1076.47 244289.23 FALSE 0
13: 3882.3 1078.81 1076.47 244289.23 FALSE 0
14: 3882.3 1078.21 1076.47 244289.23 FALSE 0
15: 3882.3 1074.34 1076.47 244289.23 FALSE 0
16: 3882.3 1076.99 1076.47 244289.23 FALSE 0
17: 3882.3 1074.20 1076.47 244289.23 FALSE 0
18: 3882.3 1069.30 1076.47 244289.23 FALSE 0
19: 3882.3 1077.81 1076.47 244289.23 FALSE 0
20: 3882.3 1078.49 1076.47 244289.23 FALSE 0
21: 1044.3 315.69 312.80 124394.23 FALSE 0
22: 1044.3 314.69 312.80 124394.23 FALSE 0
23: 1044.3 308.64 312.80 124394.23 FALSE 0
24: 1044.3 315.79 312.80 124394.23 FALSE 0
25: 1044.3 310.03 312.80 124394.23 FALSE 0
26: 1044.3 305.80 312.80 124394.23 FALSE 0
27: 1044.3 315.74 312.80 124394.23 FALSE 0
28: 1044.3 315.69 312.80 124394.23 FALSE 0
29: 1044.3 315.93 312.80 124394.23 FALSE 0
30: 1044.3 310.03 312.80 124394.23 FALSE 0
31: 1867.9 829.51 829.59 144900.44 FALSE 0
32: 1867.9 830.89 829.59 144900.44 FALSE 0
33: 1867.9 831.07 829.59 144900.44 FALSE 0
34: 1867.9 825.21 829.59 144900.44 FALSE 0
35: 1867.9 831.47 829.59 144900.44 FALSE 0
36: 1867.9 831.37 829.59 144900.44 FALSE 0
37: 1867.9 830.30 829.59 144900.44 FALSE 0
38: 1867.9 829.28 829.59 144900.44 FALSE 0
39: 1867.9 825.98 829.59 144900.44 FALSE 0
40: 1867.9 830.78 829.59 144900.44 FALSE 0
41: 197.8 61.25 65.67 102654.97 FALSE 0
42: 197.8 68.57 65.67 102654.97 FALSE 0
43: 197.8 69.70 65.67 102654.97 FALSE 0
44: 197.8 46.66 65.67 102654.97 FALSE 0
45: 197.8 69.87 65.67 102654.97 FALSE 0
46: 197.8 69.83 65.67 102654.97 FALSE 0
47: 197.8 69.75 65.67 102654.97 FALSE 0
48: 197.8 69.82 65.67 102654.97 FALSE 0
49: 197.8 68.25 65.67 102654.97 FALSE 0
50: 197.8 63.00 65.67 102654.97 FALSE 0
51: 117.7 53.49 51.78 64681.51 FALSE 0
52: 117.7 53.21 51.78 64681.51 FALSE 0
53: 117.7 49.18 51.78 64681.51 FALSE 0
54: 117.7 53.54 51.78 64681.51 FALSE 0
55: 117.7 50.67 51.78 64681.51 FALSE 0
56: 117.7 52.37 51.78 64681.51 FALSE 0
57: 117.7 52.67 51.78 64681.51 FALSE 0
58: 117.7 52.24 51.78 64681.51 FALSE 0
59: 117.7 52.71 51.78 64681.51 FALSE 0
60: 117.7 47.69 51.78 64681.51 FALSE 0
61: 6546.2 184.39 176.16 153439.14 FALSE 0
62: 6546.2 186.59 176.16 153439.14 FALSE 0
63: 6546.2 188.64 176.16 153439.14 FALSE 0
64: 6546.2 141.84 176.16 153439.14 FALSE 0
65: 6546.2 189.02 176.16 153439.14 FALSE 0
66: 6546.2 189.02 176.16 153439.14 FALSE 0
67: 6546.2 126.08 176.16 153439.14 FALSE 0
68: 6546.2 177.99 176.16 153439.14 FALSE 0
69: 6546.2 188.91 176.16 153439.14 FALSE 0
70: 6546.2 189.11 176.16 153439.14 FALSE 0
71: 3844.4 1416.78 1416.38 107550.29 FALSE 0
72: 3844.4 1412.93 1416.38 107550.29 FALSE 0
73: 3844.4 1417.86 1416.38 107550.29 FALSE 0
74: 3844.4 1416.62 1416.38 107550.29 FALSE 0
75: 3844.4 1415.80 1416.38 107550.29 FALSE 0
76: 3844.4 1415.73 1416.38 107550.29 FALSE 0
77: 3844.4 1418.01 1416.38 107550.29 FALSE 0
78: 3844.4 1417.38 1416.38 107550.29 FALSE 0
79: 3844.4 1417.21 1416.38 107550.29 FALSE 0
80: 3844.4 1415.45 1416.38 107550.29 FALSE 0
81: 414.1 83.20 79.79 176319.66 FALSE 0
82: 414.1 82.66 79.79 176319.66 FALSE 0
83: 414.1 80.48 79.79 176319.66 FALSE 0
84: 414.1 66.86 79.79 176319.66 FALSE 0
85: 414.1 83.32 79.79 176319.66 FALSE 0
86: 414.1 83.55 79.79 176319.66 FALSE 0
87: 414.1 69.65 79.79 176319.66 FALSE 0
88: 414.1 82.55 79.79 176319.66 FALSE 0
89: 414.1 82.90 79.79 176319.66 FALSE 0
90: 414.1 82.75 79.79 176319.66 FALSE 0
91: 3068.0 646.91 643.74 201806.58 FALSE 0
92: 3068.0 647.91 643.74 201806.58 FALSE 0
93: 3068.0 643.96 643.74 201806.58 FALSE 0
94: 3068.0 617.33 643.74 201806.58 FALSE 0
95: 3068.0 647.85 643.74 201806.58 FALSE 0
96: 3068.0 648.17 643.74 201806.58 FALSE 0
97: 3068.0 647.57 643.74 201806.58 FALSE 0
98: 3068.0 647.87 643.74 201806.58 FALSE 0
99: 3068.0 646.12 643.74 201806.58 FALSE 0
100: 3068.0 643.67 643.74 201806.58 FALSE 0
meanRawcounts normcounts meanCorrected theta aberrant AberrantBySample
AberrantByGene padj_rank
<num> <num>
1: 0 5.5
2: 0 5.5
3: 0 5.5
4: 0 5.5
5: 0 5.5
6: 0 5.5
7: 0 5.5
8: 0 5.5
9: 0 5.5
10: 0 5.5
11: 0 5.5
12: 0 5.5
13: 0 5.5
14: 0 5.5
15: 0 5.5
16: 0 5.5
17: 0 5.5
18: 0 5.5
19: 0 5.5
20: 0 5.5
21: 0 5.5
22: 0 5.5
23: 0 5.5
24: 0 5.5
25: 0 5.5
26: 0 5.5
27: 0 5.5
28: 0 5.5
29: 0 5.5
30: 0 5.5
31: 0 5.5
32: 0 5.5
33: 0 5.5
34: 0 5.5
35: 0 5.5
36: 0 5.5
37: 0 5.5
38: 0 5.5
39: 0 5.5
40: 0 5.5
41: 0 5.5
42: 0 5.5
43: 0 5.5
44: 0 5.5
45: 0 5.5
46: 0 5.5
47: 0 5.5
48: 0 5.5
49: 0 5.5
50: 0 5.5
51: 0 5.5
52: 0 5.5
53: 0 5.5
54: 0 5.5
55: 0 5.5
56: 0 5.5
57: 0 5.5
58: 0 5.5
59: 0 5.5
60: 0 5.5
61: 0 5.5
62: 0 5.5
63: 0 5.5
64: 0 5.5
65: 0 5.5
66: 0 5.5
67: 0 5.5
68: 0 5.5
69: 0 5.5
70: 0 5.5
71: 0 5.5
72: 0 5.5
73: 0 5.5
74: 0 5.5
75: 0 5.5
76: 0 5.5
77: 0 5.5
78: 0 5.5
79: 0 5.5
80: 0 5.5
81: 0 5.5
82: 0 5.5
83: 0 5.5
84: 0 5.5
85: 0 5.5
86: 0 5.5
87: 0 5.5
88: 0 5.5
89: 0 5.5
90: 0 5.5
91: 0 5.5
92: 0 5.5
93: 0 5.5
94: 0 5.5
95: 0 5.5
96: 0 5.5
97: 0 5.5
98: 0 5.5
99: 0 5.5
100: 0 5.5
AberrantByGene padj_rank
>
> plotAberrantPerSample(ods)
Warning in scale_y_log10(limits = c(oneOffset, NA)) :
log-10 transformation introduced infinite values.
Warning: Removed 10 rows containing missing values or values outside the scale range
(`geom_bar()`).
> plotVolcano(ods, 1)
Error in pm[[2]] : subscript out of bounds
Calls: plotVolcano ... plotVolcano -> .local -> ggplotly -> ggplotly.ggplot -> gg2list
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_plotting.R:21:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─OUTRIDER::plotVolcano(ods, 30)
5. └─OUTRIDER::plotVolcano(ods, 30)
6. └─OUTRIDER (local) .local(object, ...)
7. ├─plotly::ggplotly(p, tooltip = "text")
8. └─plotly:::ggplotly.ggplot(p, tooltip = "text")
9. └─plotly::gg2list(...)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘OUTRIDER’ ... ** this is package ‘OUTRIDER’ version ‘1.26.3’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -Werror=format-security -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OUTRIDER/00new/OUTRIDER/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OUTRIDER)
OUTRIDER.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
Type 'q()' to quit R.
> library(testthat)
> library(OUTRIDER)
Loading required package: BiocParallel
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:SummarizedExperiment':
shift
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
>
> register(SerialParam())
>
> test_check("OUTRIDER")
[1] "Tue Oct 14 12:25:12 2025: Initial PCA loss: 6.269466444026"
[1] "Tue Oct 14 12:25:14 2025: Iteration: 1 loss: 4.61577601938473"
[1] "Tue Oct 14 12:25:15 2025: Iteration: 2 loss: 4.55515474101613"
[1] "Tue Oct 14 12:25:16 2025: Iteration: 3 loss: 4.51373526295885"
[1] "Tue Oct 14 12:25:17 2025: Iteration: 4 loss: 4.48283487981497"
[1] "Tue Oct 14 12:25:17 2025: Iteration: 5 loss: 4.46743909110935"
[1] "Tue Oct 14 12:25:18 2025: Iteration: 6 loss: 4.46542241472605"
Time difference of 5.551991 secs
[1] "Tue Oct 14 12:25:18 2025: 6 Final nb-AE loss: 4.46542241472605"
[1] "Tue Oct 14 12:25:20 2025: Initial PCA loss: 6.269466444026"
[1] "Tue Oct 14 12:25:21 2025: Iteration: 1 loss: 4.61577601938473"
[1] "Tue Oct 14 12:25:22 2025: Iteration: 2 loss: 4.55515474101613"
[1] "Tue Oct 14 12:25:23 2025: Iteration: 3 loss: 4.51373526295885"
[1] "Tue Oct 14 12:25:24 2025: Iteration: 4 loss: 4.48283487981497"
[1] "Tue Oct 14 12:25:25 2025: Iteration: 5 loss: 4.46743909110935"
[1] "Tue Oct 14 12:25:26 2025: Iteration: 6 loss: 4.46542241472605"
Time difference of 5.365014 secs
[1] "Tue Oct 14 12:25:26 2025: 6 Final nb-AE loss: 4.46542241472605"
class: OutriderDataSet
class: RangedSummarizedExperiment
dim: 100 50
metadata(1): version
assays(1): counts
rownames(100): ENSG00000223972.4 ENSG00000227232.4 ...
ENSG00000107404.13 ENSG00000162576.12
rowData names(0):
colnames(50): GTEX.UPK5.0426.SM.3GAEK GTEX.WFG7.2026.SM.3GIL7 ...
GTEX.11UD2.2526.SM.5CVNU GTEX.13O61.1426.SM.5KM3D
colData names(1): sampleID
[1] "Tue Oct 14 12:25:34 2025: Initial PCA loss: 4.45497702648287"
[1] "Tue Oct 14 12:25:36 2025: Iteration: 1 loss: 4.10212714917902"
[1] "Tue Oct 14 12:25:37 2025: Iteration: 2 loss: 4.08520151065717"
Time difference of 1.875806 secs
[1] "Tue Oct 14 12:25:37 2025: 2 Final nb-AE loss: 4.08520151065717"
[1] "Evaluation loss: 0.409365624668786 for q=3"
[1] "Tue Oct 14 12:25:38 2025: Initial PCA loss: 4.42698071615731"
[1] "Tue Oct 14 12:25:40 2025: Iteration: 1 loss: 4.02209565570526"
[1] "Tue Oct 14 12:25:41 2025: Iteration: 2 loss: 4.00839830497134"
Time difference of 1.933573 secs
[1] "Tue Oct 14 12:25:41 2025: 2 Final nb-AE loss: 4.00839830497134"
[1] "Evaluation loss: 0.422585264564871 for q=4"
[1] "Tue Oct 14 12:25:42 2025: Initial PCA loss: 4.40759694007152"
[1] "Tue Oct 14 12:25:43 2025: Iteration: 1 loss: 3.94101914633159"
[1] "Tue Oct 14 12:25:44 2025: Iteration: 2 loss: 3.92229871820955"
Time difference of 1.899659 secs
[1] "Tue Oct 14 12:25:44 2025: 2 Final nb-AE loss: 3.92229871820955"
[1] "Evaluation loss: 0.380595225546335 for q=5"
Optimal encoding dimension: 4
Optimal encoding dimension: 50
Optimal encoding dimension: 20
Optimal encoding dimension: 2
Optimal encoding dimension: 4
[1] "Tue Oct 14 12:26:22 2025: Initial PCA loss: 7.16457134714849"
[1] "Tue Oct 14 12:26:24 2025: Iteration: 1 loss: 6.82913931405131"
[1] "Tue Oct 14 12:26:25 2025: Iteration: 2 loss: 6.82749008590827"
Time difference of 2.423867 secs
[1] "Tue Oct 14 12:26:25 2025: 2 Final nb-AE loss: 6.82749008590827"
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_plotting.R:21:5'): plotting ────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_plotting.R:21:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─OUTRIDER::plotVolcano(ods, 30)
5. └─OUTRIDER::plotVolcano(ods, 30)
6. └─OUTRIDER (local) .local(object, ...)
7. ├─plotly::ggplotly(p, tooltip = "text")
8. └─plotly:::ggplotly.ggplot(p, tooltip = "text")
9. └─plotly::gg2list(...)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ]
Error: Test failures
Execution halted
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed |