| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:42 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 shinyMethyl package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/shinyMethyl.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1878/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| shinyMethyl 1.37.0 (landing page) Jean-Philippe Fortin
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: shinyMethyl |
| Version: 1.37.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:shinyMethyl.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings shinyMethyl_1.37.0.tar.gz |
| StartedAt: 2023-06-06 06:52:05 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 07:00:54 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 529.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: shinyMethyl.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:shinyMethyl.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings shinyMethyl_1.37.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/shinyMethyl.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘shinyMethyl/DESCRIPTION’ ... OK
* this is package ‘shinyMethyl’ version ‘1.37.0’
* 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 ‘shinyMethyl’ 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 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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shinySummarize-methods 49.085 0.963 50.12
* 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. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/cn.Y.rds'.
1/1 mismatches
x[1]: "9b6239a1a91af3a246ad4d0c93812bf2"
y[1]: "9d0728b5c38af968a99e3d63665d4f59"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
[ FAIL 25 | WARN 26 | SKIP 0 | PASS 28 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘shinyMethyl.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.18-bioc/meat/shinyMethyl.Rcheck/00check.log’
for details.
shinyMethyl.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL shinyMethyl ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘shinyMethyl’ ... ** 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 (shinyMethyl)
shinyMethyl.Rcheck/tests/testthat.Rout.fail
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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(shinyMethyl)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("shinyMethyl")
[shinySummarize] Extracting Red and Green channels
[shinySummarize] Raw preprocessing
[shinySummarize] Mapping to genome
[shinySummarize] Computing quantiles
[shinySummarize] Computing principal components
[ FAIL 25 | WARN 26 | SKIP 0 | PASS 28 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/beta.IGrn.rds'.
1/1 mismatches
x[1]: "1c0a1b5258d36fc2b7fc57987c647524"
y[1]: "38a4407a3b9c425b755e28413a8eaba1"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/beta.IRed.rds'.
1/1 mismatches
x[1]: "b92bc1d770394d99ef6a94eaf1a54a3e"
y[1]: "b07a751cea1f683b7610e10e8085d579"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/beta.II.rds'.
1/1 mismatches
x[1]: "b21fa0bd820b8e27b32381fc2a5f7ab4"
y[1]: "4daf9b3644ada4e665762155246c519a"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/beta.X.rds'.
1/1 mismatches
x[1]: "0a902a61a8073c5bc52adc5dd079fa25"
y[1]: "d35741dd9dbef4b0d32c9b70d89c6291"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/beta.Y.rds'.
1/1 mismatches
x[1]: "d6f787f4847b74a330e0a43917cca021"
y[1]: "307c431fc8c1c5511d5507a524aeca40"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/m.IGrn.rds'.
1/1 mismatches
x[1]: "02f8aa5c0a4dfdfa4c24b31c6ef724a9"
y[1]: "abe8c88ede948543bde084b4dab03bf5"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/m.IRed.rds'.
1/1 mismatches
x[1]: "7371f3b784bd6ea4d7168e1dc31362fb"
y[1]: "ea494199ba427a549c9d0d06420fd255"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/m.II.rds'.
1/1 mismatches
x[1]: "71935d786fb70164dd5dc1b53846437f"
y[1]: "b7489cc43af3c44f8a51ccc6c95e9392"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/m.X.rds'.
1/1 mismatches
x[1]: "f10638b55516db5bf98fe628050d64e8"
y[1]: "cd218011f165b99d23f49d9c8b8545f3"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/m.Y.rds'.
1/1 mismatches
x[1]: "0665cf1a3d1cb82ce7ef9b8637cfdbef"
y[1]: "627d34cb152160c67ae500343c580073"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/meth.IGrn.rds'.
1/1 mismatches
x[1]: "17988bd59f45f28a09a795ab7e9b12d3"
y[1]: "24fae2d5a19acd6e1ba5ffe4af94186c"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/meth.IRed.rds'.
1/1 mismatches
x[1]: "407d5c8f42a958697278456105bd2bb8"
y[1]: "7b072bdfc519055b2bebba0278a2f743"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/meth.II.rds'.
1/1 mismatches
x[1]: "df9e1a138bebe1861823bc5d362fb66c"
y[1]: "91baf64875a0cd4cc46243aae5d59c71"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/meth.X.rds'.
1/1 mismatches
x[1]: "26039e8696bec5e3007208d2c69dc899"
y[1]: "0947c2b89636b37effb8fc33530658a6"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/meth.Y.rds'.
1/1 mismatches
x[1]: "2c7718f276238606d09de8c787fc04df"
y[1]: "249ee134c6f60ef4970dd0ba094de49f"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/unmeth.IGrn.rds'.
1/1 mismatches
x[1]: "626fd432ef630b29b1b3503e4ee44afc"
y[1]: "225be0db95b81409083fa98b649a1ba1"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/unmeth.IRed.rds'.
1/1 mismatches
x[1]: "3e9b50c728886ea2690cb06f57993e0c"
y[1]: "6ccd31d401b6a81558240bb31d43bdb0"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/unmeth.II.rds'.
1/1 mismatches
x[1]: "c9433f0823cba639b54985dd573c727d"
y[1]: "cae60fda290600d051938c81f7772b69"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/unmeth.X.rds'.
1/1 mismatches
x[1]: "5f9f7ad864ce673dede48590c57a3045"
y[1]: "9c9440ec7ff1e9e122a60c1eb6fe874c"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/unmeth.Y.rds'.
1/1 mismatches
x[1]: "55563f5e23899c793e929ef7909f060a"
y[1]: "db30773b70829930e9f17b7843f3d912"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/cn.IGrn.rds'.
1/1 mismatches
x[1]: "6e1a52d2e811a4b8bfabfc162217ea38"
y[1]: "24e87ea23f6097899a6ea277b0d97cf6"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/cn.IRed.rds'.
1/1 mismatches
x[1]: "e8be96352988d31a519ffb1be3ed8160"
y[1]: "aa8b1d09eb0761984caf7ad1d133371f"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/cn.II.rds'.
1/1 mismatches
x[1]: "17f9fc0b2ce83211149527862d6c66c0"
y[1]: "9e98e6297a89e62c6e98ebe9244f0ad7"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/cn.X.rds'.
1/1 mismatches
x[1]: "ea66ecfc80d2deeb56f81d317284a1ff"
y[1]: "313f2bbc14c9972a8745aaa74662ab1b"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
── Failure ('test-shinySummarize.R:29:9'): shinySummarize function ─────────────
currentDigests[[i]] has changed from known value recorded in 'objects/cn.Y.rds'.
1/1 mismatches
x[1]: "9b6239a1a91af3a246ad4d0c93812bf2"
y[1]: "9d0728b5c38af968a99e3d63665d4f59"
Backtrace:
▆
1. └─testthat::expect_equal_to_reference(currentDigests[[i]], file = file) at test-shinySummarize.R:29:8
2. └─testthat::expect_known_value(..., update = update)
[ FAIL 25 | WARN 26 | SKIP 0 | PASS 28 ]
Error: Test failures
Execution halted
shinyMethyl.Rcheck/shinyMethyl-Ex.timings
| name | user | system | elapsed | |
| runShinyMethyl | 0 | 0 | 0 | |
| shinyMethylSet-class | 0.001 | 0.000 | 0.001 | |
| shinySummarize-methods | 49.085 | 0.963 | 50.120 | |