Matteo Tiberti
| Snapshot Date: 2025-05-01 13:40 -0400 (Thu, 01 May 2025) |
| git_url: https://git.bioconductor.org/packages/Moonlight2R |
| git_branch: RELEASE_3_21 |
| git_last_commit: 8faf1a1 |
| git_last_commit_date: 2025-04-15 13:21:13 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-05-05 11:39 -0400 (Mon, 05 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4832 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4574 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4553 |
| 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 1335/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Moonlight2R 1.6.0 (landing page) Matteo Tiberti
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the Moonlight2R package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Moonlight2R.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: Moonlight2R |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Moonlight2R_1.6.0.tar.gz |
| StartedAt: 2025-05-05 00:27:49 -0400 (Mon, 05 May 2025) |
| EndedAt: 2025-05-05 00:39:01 -0400 (Mon, 05 May 2025) |
| EllapsedTime: 671.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Moonlight2R.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Moonlight2R_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 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 ‘Moonlight2R’ 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 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
TFinfluence: no visible binding for global variable ‘HGVSp_Short’
TFinfluence : <anonymous>: no visible binding for global variable
‘mutation’
TFinfluence : <anonymous>: no visible binding for global variable
‘stab_class’
TFinfluence: no visible binding for global variable ‘GENE’
TFinfluence: no visible binding for global variable ‘Target’
TFinfluence: no visible binding for global variable ‘TF’
TFinfluence: no visible binding for global variable ‘mutation’
TFinfluence: no visible binding for global variable ‘protein’
TFinfluence: no visible binding for global variable ‘tf_mutation’
TFinfluence: no visible binding for global variable ‘InteractionType’
TFinfluence: no visible binding for global variable ‘stab_class’
TFinfluence: no visible binding for global variable ‘logFC_target’
loadMAVISp: no visible binding for global variable ‘filepath’
Undefined global functions or variables:
GENE HGVSp_Short InteractionType TF Target filepath logFC_target
mutation protein stab_class tf_mutation
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GMA 87.24 13.101 104.782
* 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:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-GMA.R:14:1'): (code run outside of `test_that()`) ──────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'i' in selecting a method for function '[': invalid argument type
Backtrace:
▆
1. ├─Moonlight2R::GMA(...) at test-GMA.R:14:1
2. │ └─EpiMix::EpiMix(...)
3. │ └─EpiMix:::getFeatureProbe(met.platform = met.platform, genome = genome)
4. │ └─probe[!probe$MASK_general, ]
5. └─base::.handleSimpleError(`<fn>`, "invalid argument type", base::quote(!probe$MASK_general))
6. └─base (local) h(simpleError(msg, call))
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 61 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Moonlight2R.Rmd’ using rmarkdown
Quitting from Moonlight2R.Rmd:738-758 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `data.frame()`:
! arguments imply differing number of rows: 1758481, 0
---
Backtrace:
▆
1. └─Moonlight2R::GMA(...)
2. └─EpiMix::EpiMix(...)
3. └─EpiMix:::filterProbes(...)
4. └─EpiMix:::getProbeAnnotation(...)
5. └─base::data.frame(probe = names(manifest), gene = manifest$gene)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
arguments imply differing number of rows: 1758481, 0
--- failed re-building ‘Moonlight2R.Rmd’
SUMMARY: processing the following file failed:
‘Moonlight2R.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/Moonlight2R.Rcheck/00check.log’
for details.
Moonlight2R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Moonlight2R ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Moonlight2R’ ... ** this is package ‘Moonlight2R’ version ‘1.6.0’ ** using staged installation ** R ** data ** 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 (Moonlight2R)
Moonlight2R.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 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.
Type 'q()' to quit R.
> # 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(Moonlight2R)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("Moonlight2R")
[1] "Output folder already exists"
loading from cache
require("rtracklayer")
[1] "CScape_somatic files have been found in results-folder."
loading from cache
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Processing PubMed data ............. done!
Running Regular mode...
Fetching probe annotation...
sesameData not installed.
Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Found 13 samples with both methylation and gene expression data.
Modeling gene expression...
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Found 73 transcriptionally predictive probes.
Found 17 samples in group.1 and 6 samples in group.2
Starting Beta mixture modeling.
Running Beta mixture model on 73 probes and on 17 samples.
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Found 73 differentially methylated CpGs
Identifying functional CpG-gene pairs...
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Found 84 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
Running Enhancer mode...
Fetching probe annotation...
sesameData not installed.
Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Found 17 samples in group.1 and 6 samples in group.2
Fetching enhancer CpGs from Roadmap Epigenomics...
Downloading chromatin states from the Roadmap Epigenomics...
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB
Identifed 65057 enhancer CpGs from the epigenome E096
sesameData not installed.
Full functionality, documentation, and loading of data might not be possible without installing
downloading 1 resources
retrieving 1 resource
loading from cache
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[ FAIL 1 | WARN 3 | SKIP 0 | PASS 61 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-GMA.R:14:1'): (code run outside of `test_that()`) ──────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'i' in selecting a method for function '[': invalid argument type
Backtrace:
▆
1. ├─Moonlight2R::GMA(...) at test-GMA.R:14:1
2. │ └─EpiMix::EpiMix(...)
3. │ └─EpiMix:::getFeatureProbe(met.platform = met.platform, genome = genome)
4. │ └─probe[!probe$MASK_general, ]
5. └─base::.handleSimpleError(`<fn>`, "invalid argument type", base::quote(!probe$MASK_general))
6. └─base (local) h(simpleError(msg, call))
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 61 ]
Error: Test failures
Execution halted
Moonlight2R.Rcheck/Moonlight2R-Ex.timings
| name | user | system | elapsed | |
| DMA | 0 | 0 | 0 | |
| FEA | 0.333 | 0.005 | 0.338 | |
| GLS | 2.658 | 1.245 | 4.287 | |
| GMA | 87.240 | 13.101 | 104.782 | |
| GRN | 0.055 | 0.011 | 0.053 | |
| GSEA | 2.928 | 0.874 | 3.933 | |
| LPA | 0.168 | 0.002 | 0.170 | |
| LiftMAF | 3.218 | 0.875 | 4.586 | |
| MAFtoCscape | 0.042 | 0.003 | 0.045 | |
| PRA | 0.156 | 0.001 | 0.157 | |
| PRAtoTibble | 0.031 | 0.008 | 0.039 | |
| RunCscape_somatic | 0.000 | 0.006 | 0.006 | |
| TFinfluence | 0.175 | 0.024 | 0.200 | |
| URA | 1.385 | 0.206 | 1.594 | |
| confidence | 0.000 | 0.000 | 0.001 | |
| getDataGEO | 2.681 | 0.458 | 4.069 | |
| loadMAVISp | 0.148 | 0.156 | 0.300 | |
| moonlight | 0 | 0 | 0 | |
| plotCircos | 0.749 | 0.110 | 0.863 | |
| plotDMA | 3.095 | 0.520 | 3.628 | |
| plotFEA | 0.321 | 0.007 | 0.328 | |
| plotGMA | 3.804 | 0.637 | 4.463 | |
| plotMetExp | 1.392 | 0.153 | 1.551 | |
| plotMoonlight | 1.634 | 0.115 | 1.751 | |
| plotMoonlightMet | 0.963 | 0.104 | 1.068 | |
| plotNetworkHive | 0.028 | 0.004 | 0.032 | |
| plotURA | 0.200 | 0.006 | 0.206 | |
| tabix_func | 0 | 0 | 0 | |