| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:19 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the OUTRIDER package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1409/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.17.1 (landing page) Christian Mertes
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: OUTRIDER |
| Version: 1.17.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings OUTRIDER_1.17.1.tar.gz |
| StartedAt: 2023-02-07 10:33:14 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 10:44:25 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 670.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings OUTRIDER_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.17.1’
* 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 ‘OUTRIDER’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 R 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 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 ... NOTE
padjOnSubset: no visible global function definition for ‘bpmapply’
Undefined global functions or variables:
bpmapply
* 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 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 Feb 7 10:40:43 2023: SizeFactor estimation ...
Tue Feb 7 10:40:43 2023: Controlling for confounders ...
Using provided q with: 10
Tue Feb 7 10:40:43 2023: Using the pca implementation for controlling.
Tue Feb 7 10:40:43 2023: Used the pca implementation for controlling.
Tue Feb 7 10:40:43 2023: Fitting the data ...
Tue Feb 7 10:40:49 2023: P-value calculation ...
Tue Feb 7 10:40:50 2023: 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 0.9956328 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 0.9899074 0.8672567 1.0000000 1.0000000 0.8466524
feature_7 0.9996621 0.9941735 0.9987931 0.9951721 0.9949311 0.9736960
feature_8 1.0000000 0.9589016 0.8852729 1.0000000 0.9101461 0.8960677
feature_9 0.9944175 0.9819508 0.9432241 1.0000000 0.9670230 1.0000000
feature_10 1.0000000 0.9714403 1.0000000 0.9861801 0.9942400 0.9858725
sample_7 sample_8 sample_9 sample_10
feature_1 0.9654920 1.0000000 0.9479204 0.9599123
feature_2 1.0000000 0.9600618 0.9691272 0.9950101
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 0.9962630 0.9703483 0.9706845
feature_7 1.0000000 1.0000000 0.9939857 0.9878664
feature_8 0.9879652 0.9976097 0.9930989 0.9906877
feature_9 1.0000000 0.9898412 0.9810968 1.0000000
feature_10 0.9773058 0.9987815 1.0000000 1.0000000
> res <- results(ods, all=TRUE)
> res
geneID sampleID pValue padjust zScore l2fc rawcounts normcounts
1: feature_1 sample_1 0.9708112 1 -0.26 -0.02 58 242.52
2: feature_2 sample_1 1.0000000 1 0.76 0.00 1033 315.69
3: feature_3 sample_1 0.9956214 1 -0.04 0.00 404 829.51
4: feature_4 sample_1 0.9172160 1 -0.67 -0.17 7 61.25
5: feature_5 sample_1 0.9341059 1 0.88 0.00 336 53.49
6: feature_6 sample_1 0.9589618 1 0.35 -0.04 39 184.39
7: feature_7 sample_1 0.9996621 1 0.27 0.00 1095 1416.78
8: feature_8 sample_1 1.0000000 1 0.56 -0.01 217 83.20
9: feature_9 sample_1 0.9944175 1 0.34 0.00 503 646.91
10: feature_10 sample_1 1.0000000 1 0.54 0.00 1449 1078.11
11: feature_1 sample_2 0.9673898 1 -0.46 -0.03 49 241.77
12: feature_2 sample_2 0.9645359 1 -1.10 -0.03 42 308.64
13: feature_3 sample_2 1.0000000 1 0.67 0.00 1690 831.07
14: feature_4 sample_2 1.0000000 1 0.57 -0.01 235 69.70
15: feature_5 sample_2 0.9465044 1 -1.33 -0.12 11 49.18
16: feature_6 sample_2 0.9899074 1 0.56 0.00 398 188.64
17: feature_7 sample_2 0.9941735 1 0.99 0.00 6690 1417.86
18: feature_8 sample_2 0.9589016 1 0.09 -0.05 26 80.48
19: feature_9 sample_2 0.9819508 1 0.02 -0.01 152 643.96
20: feature_10 sample_2 0.9714403 1 0.77 0.00 27702 1078.81
21: feature_1 sample_3 1.0000000 1 0.74 0.00 434 246.13
22: feature_2 sample_3 0.9956328 1 0.79 0.00 1592 315.79
23: feature_3 sample_3 0.9817906 1 -1.96 -0.01 130 825.21
24: feature_4 sample_3 0.8531784 1 -2.53 -0.42 2 46.66
25: feature_5 sample_3 0.8974455 1 0.91 0.00 497 53.54
26: feature_6 sample_3 0.8672567 1 -1.54 -0.32 3 141.84
27: feature_7 sample_3 0.9987931 1 0.16 0.00 980 1416.62
28: feature_8 sample_3 0.8852729 1 -2.08 -0.26 4 66.86
29: feature_9 sample_3 0.9432241 1 -2.80 -0.07 20 617.33
30: feature_10 sample_3 1.0000000 1 0.57 0.00 1673 1078.21
31: feature_1 sample_4 1.0000000 1 0.83 0.00 1052 246.47
32: feature_2 sample_4 0.9691272 1 -0.74 -0.03 52 310.03
33: feature_3 sample_4 0.9714409 1 0.84 0.00 8658 831.47
34: feature_4 sample_4 0.9520697 1 0.59 0.00 541 69.87
35: feature_5 sample_4 0.9659065 1 -0.58 -0.08 17 50.67
36: feature_6 sample_4 1.0000000 1 0.58 0.00 2050 189.02
37: feature_7 sample_4 0.9951721 1 -0.39 0.00 623 1415.80
38: feature_8 sample_4 1.0000000 1 0.58 0.00 323 83.32
39: feature_9 sample_4 1.0000000 1 0.44 0.00 1830 647.85
40: feature_10 sample_4 0.9861801 1 -0.71 -0.01 238 1074.34
41: feature_1 sample_5 0.9682199 1 -0.41 -0.03 51 241.96
42: feature_2 sample_5 0.9565509 1 -1.84 -0.05 30 305.80
43: feature_3 sample_5 0.9874758 1 0.80 0.00 4329 831.37
44: feature_4 sample_5 0.9681790 1 0.59 0.00 427 69.83
45: feature_5 sample_5 1.0000000 1 0.29 -0.03 41 52.37
46: feature_6 sample_5 1.0000000 1 0.58 0.00 2075 189.02
47: feature_7 sample_5 0.9949311 1 -0.43 0.00 605 1415.73
48: feature_8 sample_5 0.9101461 1 0.62 0.00 3174 83.55
49: feature_9 sample_5 0.9670230 1 0.47 0.00 22553 648.17
50: feature_10 sample_5 0.9942400 1 0.17 0.00 580 1076.99
51: feature_1 sample_6 0.9715971 1 0.88 0.00 4121 246.64
52: feature_2 sample_6 1.0000000 1 0.78 0.00 1247 315.74
53: feature_3 sample_6 1.0000000 1 0.32 0.00 657 830.30
54: feature_4 sample_6 0.9964730 1 0.57 -0.01 278 69.75
55: feature_5 sample_6 1.0000000 1 0.45 -0.03 54 52.67
56: feature_6 sample_6 0.8466524 1 -2.16 -0.42 2 126.08
57: feature_7 sample_6 0.9736960 1 1.09 0.00 23938 1418.01
58: feature_8 sample_6 0.8960677 1 -1.66 -0.22 5 69.65
59: feature_9 sample_6 1.0000000 1 0.41 0.00 1030 647.57
60: feature_10 sample_6 0.9858725 1 -0.75 -0.01 231 1074.20
61: feature_1 sample_7 0.9654920 1 0.89 0.00 5031 246.65
62: feature_2 sample_7 1.0000000 1 0.76 0.00 1041 315.69
63: feature_3 sample_7 0.9944387 1 -0.14 0.00 363 829.28
64: feature_4 sample_7 0.9738876 1 0.58 0.00 392 69.82
65: feature_5 sample_7 0.9985055 1 0.22 -0.04 37 52.24
66: feature_6 sample_7 0.9361394 1 0.04 -0.08 16 177.99
67: feature_7 sample_7 1.0000000 1 0.67 0.00 2051 1417.38
68: feature_8 sample_7 0.9879652 1 0.44 -0.02 80 82.55
69: feature_9 sample_7 1.0000000 1 0.44 0.00 1934 647.87
70: feature_10 sample_7 0.9773058 1 -2.37 -0.01 112 1069.30
71: feature_1 sample_8 1.0000000 1 0.80 0.00 691 246.35
72: feature_2 sample_8 0.9600618 1 0.83 0.00 5113 315.93
73: feature_3 sample_8 0.9835739 1 -1.62 -0.01 148 825.98
74: feature_4 sample_8 0.9834010 1 0.34 -0.04 39 68.25
75: feature_5 sample_8 1.0000000 1 0.47 -0.03 56 52.71
76: feature_6 sample_8 0.9962630 1 0.57 0.00 939 188.91
77: feature_7 sample_8 1.0000000 1 0.56 0.00 1647 1417.21
78: feature_8 sample_8 0.9976097 1 0.51 -0.01 122 82.90
79: feature_9 sample_8 0.9898412 1 0.25 0.00 310 646.12
80: feature_10 sample_8 0.9987815 1 0.44 0.00 1036 1077.81
81: feature_1 sample_9 0.9479204 1 -2.03 -0.06 22 235.98
82: feature_2 sample_9 0.9691272 1 -0.74 -0.03 52 310.03
83: feature_3 sample_9 1.0000000 1 0.54 0.00 1062 830.78
84: feature_4 sample_9 0.9285130 1 -0.43 -0.14 9 63.00
85: feature_5 sample_9 0.9314466 1 -2.05 -0.15 8 47.69
86: feature_6 sample_9 0.9703483 1 0.58 0.00 59866 189.11
87: feature_7 sample_9 0.9939857 1 -0.62 0.00 540 1415.45
88: feature_8 sample_9 0.9930989 1 0.48 -0.01 100 82.75
89: feature_9 sample_9 0.9810968 1 -0.01 -0.01 142 643.67
90: feature_10 sample_9 1.0000000 1 0.67 0.00 2984 1078.49
91: feature_1 sample_10 0.9599123 1 -0.99 -0.04 35 239.85
92: feature_2 sample_10 0.9950101 1 0.50 -0.01 241 314.69
93: feature_3 sample_10 1.0000000 1 0.59 0.00 1238 830.89
94: feature_4 sample_10 0.9901875 1 0.39 -0.03 48 68.57
95: feature_5 sample_10 1.0000000 1 0.73 -0.01 120 53.21
96: feature_6 sample_10 0.9706845 1 0.45 -0.02 74 186.59
97: feature_7 sample_10 0.9878664 1 -2.29 -0.01 275 1412.93
98: feature_8 sample_10 0.9906877 1 0.46 -0.02 90 82.66
99: feature_9 sample_10 1.0000000 1 0.45 0.00 2206 647.91
100: feature_10 sample_10 1.0000000 1 0.66 0.00 2818 1078.47
geneID sampleID pValue padjust zScore l2fc rawcounts normcounts
meanCorrected theta aberrant AberrantBySample AberrantByGene padj_rank
1: 243.43 120193.2 FALSE 0 0 5.5
2: 312.80 124437.3 FALSE 0 0 5.5
3: 829.59 144900.2 FALSE 0 0 5.5
4: 65.67 102654.8 FALSE 0 0 5.5
5: 51.78 64681.5 FALSE 0 0 5.5
6: 176.16 153410.4 FALSE 0 0 5.5
7: 1416.38 107763.6 FALSE 0 0 5.5
8: 79.79 176265.5 FALSE 0 0 5.5
9: 643.74 201805.4 FALSE 0 0 5.5
10: 1076.47 271486.9 FALSE 0 0 5.5
11: 243.43 120193.2 FALSE 0 0 5.5
12: 312.80 124437.3 FALSE 0 0 5.5
13: 829.59 144900.2 FALSE 0 0 5.5
14: 65.67 102654.8 FALSE 0 0 5.5
15: 51.78 64681.5 FALSE 0 0 5.5
16: 176.16 153410.4 FALSE 0 0 5.5
17: 1416.38 107763.6 FALSE 0 0 5.5
18: 79.79 176265.5 FALSE 0 0 5.5
19: 643.74 201805.4 FALSE 0 0 5.5
20: 1076.47 271486.9 FALSE 0 0 5.5
21: 243.43 120193.2 FALSE 0 0 5.5
22: 312.80 124437.3 FALSE 0 0 5.5
23: 829.59 144900.2 FALSE 0 0 5.5
24: 65.67 102654.8 FALSE 0 0 5.5
25: 51.78 64681.5 FALSE 0 0 5.5
26: 176.16 153410.4 FALSE 0 0 5.5
27: 1416.38 107763.6 FALSE 0 0 5.5
28: 79.79 176265.5 FALSE 0 0 5.5
29: 643.74 201805.4 FALSE 0 0 5.5
30: 1076.47 271486.9 FALSE 0 0 5.5
31: 243.43 120193.2 FALSE 0 0 5.5
32: 312.80 124437.3 FALSE 0 0 5.5
33: 829.59 144900.2 FALSE 0 0 5.5
34: 65.67 102654.8 FALSE 0 0 5.5
35: 51.78 64681.5 FALSE 0 0 5.5
36: 176.16 153410.4 FALSE 0 0 5.5
37: 1416.38 107763.6 FALSE 0 0 5.5
38: 79.79 176265.5 FALSE 0 0 5.5
39: 643.74 201805.4 FALSE 0 0 5.5
40: 1076.47 271486.9 FALSE 0 0 5.5
41: 243.43 120193.2 FALSE 0 0 5.5
42: 312.80 124437.3 FALSE 0 0 5.5
43: 829.59 144900.2 FALSE 0 0 5.5
44: 65.67 102654.8 FALSE 0 0 5.5
45: 51.78 64681.5 FALSE 0 0 5.5
46: 176.16 153410.4 FALSE 0 0 5.5
47: 1416.38 107763.6 FALSE 0 0 5.5
48: 79.79 176265.5 FALSE 0 0 5.5
49: 643.74 201805.4 FALSE 0 0 5.5
50: 1076.47 271486.9 FALSE 0 0 5.5
51: 243.43 120193.2 FALSE 0 0 5.5
52: 312.80 124437.3 FALSE 0 0 5.5
53: 829.59 144900.2 FALSE 0 0 5.5
54: 65.67 102654.8 FALSE 0 0 5.5
55: 51.78 64681.5 FALSE 0 0 5.5
56: 176.16 153410.4 FALSE 0 0 5.5
57: 1416.38 107763.6 FALSE 0 0 5.5
58: 79.79 176265.5 FALSE 0 0 5.5
59: 643.74 201805.4 FALSE 0 0 5.5
60: 1076.47 271486.9 FALSE 0 0 5.5
61: 243.43 120193.2 FALSE 0 0 5.5
62: 312.80 124437.3 FALSE 0 0 5.5
63: 829.59 144900.2 FALSE 0 0 5.5
64: 65.67 102654.8 FALSE 0 0 5.5
65: 51.78 64681.5 FALSE 0 0 5.5
66: 176.16 153410.4 FALSE 0 0 5.5
67: 1416.38 107763.6 FALSE 0 0 5.5
68: 79.79 176265.5 FALSE 0 0 5.5
69: 643.74 201805.4 FALSE 0 0 5.5
70: 1076.47 271486.9 FALSE 0 0 5.5
71: 243.43 120193.2 FALSE 0 0 5.5
72: 312.80 124437.3 FALSE 0 0 5.5
73: 829.59 144900.2 FALSE 0 0 5.5
74: 65.67 102654.8 FALSE 0 0 5.5
75: 51.78 64681.5 FALSE 0 0 5.5
76: 176.16 153410.4 FALSE 0 0 5.5
77: 1416.38 107763.6 FALSE 0 0 5.5
78: 79.79 176265.5 FALSE 0 0 5.5
79: 643.74 201805.4 FALSE 0 0 5.5
80: 1076.47 271486.9 FALSE 0 0 5.5
81: 243.43 120193.2 FALSE 0 0 5.5
82: 312.80 124437.3 FALSE 0 0 5.5
83: 829.59 144900.2 FALSE 0 0 5.5
84: 65.67 102654.8 FALSE 0 0 5.5
85: 51.78 64681.5 FALSE 0 0 5.5
86: 176.16 153410.4 FALSE 0 0 5.5
87: 1416.38 107763.6 FALSE 0 0 5.5
88: 79.79 176265.5 FALSE 0 0 5.5
89: 643.74 201805.4 FALSE 0 0 5.5
90: 1076.47 271486.9 FALSE 0 0 5.5
91: 243.43 120193.2 FALSE 0 0 5.5
92: 312.80 124437.3 FALSE 0 0 5.5
93: 829.59 144900.2 FALSE 0 0 5.5
94: 65.67 102654.8 FALSE 0 0 5.5
95: 51.78 64681.5 FALSE 0 0 5.5
96: 176.16 153410.4 FALSE 0 0 5.5
97: 1416.38 107763.6 FALSE 0 0 5.5
98: 79.79 176265.5 FALSE 0 0 5.5
99: 643.74 201805.4 FALSE 0 0 5.5
100: 1076.47 271486.9 FALSE 0 0 5.5
meanCorrected theta aberrant AberrantBySample AberrantByGene padj_rank
FDR_set
1: transcriptome-wide
2: transcriptome-wide
3: transcriptome-wide
4: transcriptome-wide
5: transcriptome-wide
6: transcriptome-wide
7: transcriptome-wide
8: transcriptome-wide
9: transcriptome-wide
10: transcriptome-wide
11: transcriptome-wide
12: transcriptome-wide
13: transcriptome-wide
14: transcriptome-wide
15: transcriptome-wide
16: transcriptome-wide
17: transcriptome-wide
18: transcriptome-wide
19: transcriptome-wide
20: transcriptome-wide
21: transcriptome-wide
22: transcriptome-wide
23: transcriptome-wide
24: transcriptome-wide
25: transcriptome-wide
26: transcriptome-wide
27: transcriptome-wide
28: transcriptome-wide
29: transcriptome-wide
30: transcriptome-wide
31: transcriptome-wide
32: transcriptome-wide
33: transcriptome-wide
34: transcriptome-wide
35: transcriptome-wide
36: transcriptome-wide
37: transcriptome-wide
38: transcriptome-wide
39: transcriptome-wide
40: transcriptome-wide
41: transcriptome-wide
42: transcriptome-wide
43: transcriptome-wide
44: transcriptome-wide
45: transcriptome-wide
46: transcriptome-wide
47: transcriptome-wide
48: transcriptome-wide
49: transcriptome-wide
50: transcriptome-wide
51: transcriptome-wide
52: transcriptome-wide
53: transcriptome-wide
54: transcriptome-wide
55: transcriptome-wide
56: transcriptome-wide
57: transcriptome-wide
58: transcriptome-wide
59: transcriptome-wide
60: transcriptome-wide
61: transcriptome-wide
62: transcriptome-wide
63: transcriptome-wide
64: transcriptome-wide
65: transcriptome-wide
66: transcriptome-wide
67: transcriptome-wide
68: transcriptome-wide
69: transcriptome-wide
70: transcriptome-wide
71: transcriptome-wide
72: transcriptome-wide
73: transcriptome-wide
74: transcriptome-wide
75: transcriptome-wide
76: transcriptome-wide
77: transcriptome-wide
78: transcriptome-wide
79: transcriptome-wide
80: transcriptome-wide
81: transcriptome-wide
82: transcriptome-wide
83: transcriptome-wide
84: transcriptome-wide
85: transcriptome-wide
86: transcriptome-wide
87: transcriptome-wide
88: transcriptome-wide
89: transcriptome-wide
90: transcriptome-wide
91: transcriptome-wide
92: transcriptome-wide
93: transcriptome-wide
94: transcriptome-wide
95: transcriptome-wide
96: transcriptome-wide
97: transcriptome-wide
98: transcriptome-wide
99: transcriptome-wide
100: transcriptome-wide
FDR_set
>
> plotAberrantPerSample(ods)
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 10 rows containing missing values (`geom_bar()`).
> plotVolcano(ods, 1)
>
> # example of restricting FDR correction to subsets of genes of interest
> genesOfInterest <- list("sample_1"=sample(rownames(ods), 3),
+ "sample_2"=sample(rownames(ods), 8),
+ "sample_6"=sample(rownames(ods), 5))
> genesOfInterest
$sample_1
[1] "feature_10" "feature_1" "feature_6"
$sample_2
[1] "feature_8" "feature_10" "feature_4" "feature_3" "feature_6"
[6] "feature_1" "feature_2" "feature_9"
$sample_6
[1] "feature_5" "feature_6" "feature_8" "feature_10" "feature_7"
> ods <- OUTRIDER(ods, subsets=list("exampleSubset"=genesOfInterest))
Tue Feb 7 10:40:53 2023: SizeFactor estimation ...
Tue Feb 7 10:40:53 2023: Controlling for confounders ...
Using provided q with: 10
Tue Feb 7 10:40:54 2023: Using the autoencoder implementation for controlling.
[1] "Tue Feb 7 10:40:56 2023: Initial PCA loss: 6.95599736916101"
Killed
* 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:
[1] "Tue Feb 7 10:42:19 2023: 2 Final nb-AE loss: 4.14004814419489"
[1] "Evaluation loss: 0.517781423170479 for q=3"
[1] "Tue Feb 7 10:42:21 2023: Initial PCA loss: 4.4572558295302"
[1] "Tue Feb 7 10:42:24 2023: Iteration: 1 loss: 4.07122946861174"
[1] "Tue Feb 7 10:42:26 2023: Iteration: 2 loss: 4.05826513752563"
Time difference of 3.442074 secs
[1] "Tue Feb 7 10:42:26 2023: 2 Final nb-AE loss: 4.05826513752563"
[1] "Evaluation loss: 0.454717572219274 for q=4"
[1] "Tue Feb 7 10:42:27 2023: Initial PCA loss: 4.4282762368912"
[1] "Tue Feb 7 10:42:29 2023: Iteration: 1 loss: 3.9973349377491"
[1] "Tue Feb 7 10:42:30 2023: Iteration: 2 loss: 3.96432433728888"
Time difference of 2.703483 secs
[1] "Tue Feb 7 10:42:30 2023: 2 Final nb-AE loss: 3.96432433728888"
[1] "Evaluation loss: 0.426020105666412 for q=5"
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘OUTRIDER.Rnw’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘OUTRIDER.Rnw’ using knitr
The magick package is required to crop "figure/deVsOutlier-1.png" but not available.
Killed
* checking PDF version of manual ... OK
* DONE
Status: 3 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
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Type 'license()' or 'licence()' for distribution details.
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Type 'q()' to quit R.
> library(testthat)
> library(OUTRIDER)
Loading required package: BiocParallel
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
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 Feb 7 10:41:35 2023: Initial PCA loss: 6.23443546871152"
[1] "Tue Feb 7 10:41:38 2023: Iteration: 1 loss: 4.48133717042354"
[1] "Tue Feb 7 10:41:40 2023: Iteration: 2 loss: 4.42404695782621"
[1] "Tue Feb 7 10:41:41 2023: Iteration: 3 loss: 4.38477899522259"
[1] "Tue Feb 7 10:41:42 2023: Iteration: 4 loss: 4.36539405165039"
[1] "Tue Feb 7 10:41:43 2023: Iteration: 5 loss: 4.35942745103864"
[1] "Tue Feb 7 10:41:44 2023: Iteration: 6 loss: 4.35611040440345"
Time difference of 8.072001 secs
[1] "Tue Feb 7 10:41:44 2023: 6 Final nb-AE loss: 4.35611040440345"
[1] "Tue Feb 7 10:41:46 2023: Initial PCA loss: 6.23443546871152"
[1] "Tue Feb 7 10:41:48 2023: Iteration: 1 loss: 4.48133717042354"
[1] "Tue Feb 7 10:41:49 2023: Iteration: 2 loss: 4.42404695782621"
[1] "Tue Feb 7 10:41:50 2023: Iteration: 3 loss: 4.38477899522259"
[1] "Tue Feb 7 10:41:51 2023: Iteration: 4 loss: 4.36539405165039"
[1] "Tue Feb 7 10:41:52 2023: Iteration: 5 loss: 4.35942745103864"
[1] "Tue Feb 7 10:41:53 2023: Iteration: 6 loss: 4.35611040440345"
Time difference of 6.006369 secs
[1] "Tue Feb 7 10:41:53 2023: 6 Final nb-AE loss: 4.35611040440345"
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 Feb 7 10:42:15 2023: Initial PCA loss: 4.4885467635678"
[1] "Tue Feb 7 10:42:18 2023: Iteration: 1 loss: 4.15953916852321"
[1] "Tue Feb 7 10:42:19 2023: Iteration: 2 loss: 4.14004814419489"
Time difference of 3.183209 secs
[1] "Tue Feb 7 10:42:19 2023: 2 Final nb-AE loss: 4.14004814419489"
[1] "Evaluation loss: 0.517781423170479 for q=3"
[1] "Tue Feb 7 10:42:21 2023: Initial PCA loss: 4.4572558295302"
[1] "Tue Feb 7 10:42:24 2023: Iteration: 1 loss: 4.07122946861174"
[1] "Tue Feb 7 10:42:26 2023: Iteration: 2 loss: 4.05826513752563"
Time difference of 3.442074 secs
[1] "Tue Feb 7 10:42:26 2023: 2 Final nb-AE loss: 4.05826513752563"
[1] "Evaluation loss: 0.454717572219274 for q=4"
[1] "Tue Feb 7 10:42:27 2023: Initial PCA loss: 4.4282762368912"
[1] "Tue Feb 7 10:42:29 2023: Iteration: 1 loss: 3.9973349377491"
[1] "Tue Feb 7 10:42:30 2023: Iteration: 2 loss: 3.96432433728888"
Time difference of 2.703483 secs
[1] "Tue Feb 7 10:42:30 2023: 2 Final nb-AE loss: 3.96432433728888"
[1] "Evaluation loss: 0.426020105666412 for q=5"
Killed
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
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