| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-20 11:57 -0500 (Fri, 20 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4890 |
| 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 1352/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Moonlight2R 1.8.1 (landing page) Matteo Tiberti
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for Moonlight2R in R Universe. | ||||||||||||||
|
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: 1.8.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Moonlight2R_1.8.1.tar.gz |
| StartedAt: 2026-02-20 02:28:46 -0500 (Fri, 20 Feb 2026) |
| EndedAt: 2026-02-20 02:41:21 -0500 (Fri, 20 Feb 2026) |
| EllapsedTime: 755.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Moonlight2R.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Moonlight2R_1.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.8.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
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 ... INFO
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 3.9Mb
* 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’
plotHeatmap: no visible global function definition for ‘add_tile’
plotHeatmap: no visible global function definition for ‘add_bar’
Undefined global functions or variables:
GENE HGVSp_Short InteractionType TF Target add_bar add_tile 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 59.92 3.58 69.769
* 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:
2. └─EpiMix::EpiMix(...)
3. └─EpiMix:::filterProbes(...)
4. └─EpiMix:::getProbeAnnotation(...)
5. └─EpiMix::EpiMix_getInfiniumAnnotation(plat = met.platform, genome = genome)
6. └─ExperimentHub::ExperimentHub()
7. └─AnnotationHub::.Hub(...)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 48 ]
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 `value[[3L]]()`:
! failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
---
Backtrace:
▆
1. └─Moonlight2R::GMA(...)
2. └─EpiMix::EpiMix(...)
3. └─EpiMix:::filterProbes(...)
4. └─EpiMix:::getProbeAnnotation(...)
5. └─EpiMix::EpiMix_getInfiniumAnnotation(plat = met.platform, genome = genome)
6. └─ExperimentHub::ExperimentHub()
7. └─AnnotationHub::.Hub(...)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
--- 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-3.22-bioc/meat/Moonlight2R.Rcheck/00check.log’
for details.
Moonlight2R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Moonlight2R ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘Moonlight2R’ ... ** this is package ‘Moonlight2R’ version ‘1.8.1’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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"
Saving _problems/test-DMA-18.R
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Saving _problems/test-GLS-7.R
Running Regular mode...
Fetching probe annotation...
Saving _problems/test-GMA-19.R
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[ FAIL 3 | WARN 3 | SKIP 0 | PASS 48 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-DMA.R:14:1'): (code run outside of `test_that()`) ──────────────
Error in `value[[3L]](cond)`: failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
Backtrace:
▆
1. └─Moonlight2R::DMA(...) at test-DMA.R:14:1
2. └─Moonlight2R::LiftMAF(Infile = mut_only, Current_Build = "GRCh38")
3. └─AnnotationHub::AnnotationHub()
4. └─AnnotationHub::.Hub(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-GLS.R:6:1'): (code run outside of `test_that()`) ───────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map(genes, search_pubmed)`: i In index: 1.
Caused by error in `data.frame()`:
! arguments imply differing number of rows: 1, 0
Backtrace:
▆
1. ├─Moonlight2R::GLS(genes = genes_query, query_string = "AND cancer AND driver AND '1980/01/01'[Date - Publication] : '2023/01/01'[Date - Publication]") at test-GLS.R:6:1
2. │ ├─map(genes, search_pubmed) %>% bind_rows()
3. │ └─purrr::map(genes, search_pubmed)
4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
5. │ ├─purrr:::with_indexed_errors(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ ├─purrr:::call_with_cleanup(...)
8. │ └─Moonlight2R (local) .f(.x[[i]], ...)
9. │ └─easyPubMed::epm_query(pubmed_query)
10. │ └─easyPubMed:::EPM_job_split(...)
11. │ └─easyPubMed (local) compute_subquery(...)
12. │ └─base::data.frame(...)
13. │ └─base::stop(...)
14. ├─dplyr::bind_rows(.)
15. │ └─rlang::list2(...)
16. └─base::.handleSimpleError(...)
17. └─purrr (local) h(simpleError(msg, call))
18. └─cli::cli_abort(...)
19. └─rlang::abort(...)
── Error ('test-GMA.R:14:1'): (code run outside of `test_that()`) ──────────────
Error in `value[[3L]](cond)`: failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
Backtrace:
▆
1. └─Moonlight2R::GMA(...) at test-GMA.R:14:1
2. └─EpiMix::EpiMix(...)
3. └─EpiMix:::filterProbes(...)
4. └─EpiMix:::getProbeAnnotation(...)
5. └─EpiMix::EpiMix_getInfiniumAnnotation(plat = met.platform, genome = genome)
6. └─ExperimentHub::ExperimentHub()
7. └─AnnotationHub::.Hub(...)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 48 ]
Error:
! Test failures.
Execution halted
Moonlight2R.Rcheck/Moonlight2R-Ex.timings
| name | user | system | elapsed | |
| DMA | 0 | 0 | 0 | |
| FEA | 0.287 | 0.009 | 0.295 | |
| GLS | 1.083 | 0.117 | 2.861 | |
| GMA | 59.920 | 3.580 | 69.769 | |
| GRN | 0.056 | 0.000 | 0.044 | |
| GSEA | 1.224 | 0.038 | 1.428 | |
| LPA | 0.177 | 0.000 | 0.176 | |
| LiftMAF | 2.944 | 0.316 | 3.857 | |
| MAFtoCscape | 0.039 | 0.000 | 0.040 | |
| PRA | 0.156 | 0.002 | 0.158 | |
| PRAtoTibble | 0.032 | 0.001 | 0.033 | |
| RunCscape_somatic | 0 | 0 | 0 | |
| TFinfluence | 0.379 | 0.008 | 0.387 | |
| URA | 1.355 | 0.050 | 1.407 | |
| confidence | 0.000 | 0.001 | 0.000 | |
| getDataGEO | 2.589 | 0.215 | 4.100 | |
| loadMAVISp | 0.129 | 0.148 | 0.270 | |
| moonlight | 0 | 0 | 0 | |
| plotCircos | 0.729 | 0.072 | 0.803 | |
| plotDMA | 3.029 | 0.340 | 3.379 | |
| plotFEA | 0.330 | 0.002 | 0.331 | |
| plotGMA | 3.926 | 0.941 | 4.891 | |
| plotMetExp | 1.830 | 0.292 | 2.127 | |
| plotMoonlight | 1.513 | 0.219 | 1.736 | |
| plotMoonlightMet | 0.968 | 0.130 | 1.101 | |
| plotNetworkHive | 0.025 | 0.006 | 0.032 | |
| plotURA | 0.200 | 0.012 | 0.212 | |
| tabix_func | 0 | 0 | 0 | |