Matteo Tiberti
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/Moonlight2R |
| git_branch: devel |
| git_last_commit: c6d5495 |
| git_last_commit_date: 2024-12-18 10:22:24 -0500 (Wed, 18 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1300/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Moonlight2R 1.5.2 (landing page) Matteo Tiberti
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Moonlight2R |
| Version: 1.5.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Moonlight2R_1.5.2.tar.gz |
| StartedAt: 2024-12-24 08:49:44 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 09:04:34 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 889.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Moonlight2R.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Moonlight2R_1.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Moonlight2R.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.5.2’
* 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/Moonlight2R.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 5.1Mb
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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ‘in_MAVISp’
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 in_MAVISp
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
Undocumented data sets:
‘dataMAVISp’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 112.702 7.638 148.589
plotGMA 6.578 0.982 7.579
plotDMA 5.695 0.831 6.542
LiftMAF 4.293 0.364 7.979
GLS 2.891 1.197 6.772
getDataGEO 2.673 0.354 13.137
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 5 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/Moonlight2R.Rcheck/00check.log’
for details.
Moonlight2R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Moonlight2R ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘Moonlight2R’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (Moonlight2R)
Moonlight2R.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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.
> # 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
Warning: program compiled against libxml 212 using older 211
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
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|====== | 8%
|
|====== | 9%
|
|======= | 10%
|
|======== | 11%
|
|======== | 12%
|
|========= | 13%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 19%
|
|============== | 20%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 29%
|
|===================== | 30%
|
|===================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 39%
|
|============================ | 40%
|
|============================ | 41%
|
|============================= | 42%
|
|============================== | 43%
|
|============================== | 44%
|
|=============================== | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|===================================== | 52%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 55%
|
|======================================== | 56%
|
|======================================== | 57%
|
|========================================= | 58%
|
|========================================== | 59%
|
|========================================== | 60%
|
|=========================================== | 61%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================== | 65%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================= | 69%
|
|================================================= | 70%
|
|================================================== | 71%
|
|=================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 77%
|
|======================================================= | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 81%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
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...
|
| | 0%
|
|= | 1%
|
|== | 3%
|
|=== | 4%
|
|==== | 5%
|
|===== | 7%
|
|====== | 8%
|
|======= | 10%
|
|======== | 11%
|
|========= | 12%
|
|========== | 14%
|
|=========== | 15%
|
|============ | 16%
|
|============ | 18%
|
|============= | 19%
|
|============== | 21%
|
|=============== | 22%
|
|================ | 23%
|
|================= | 25%
|
|================== | 26%
|
|=================== | 27%
|
|==================== | 29%
|
|===================== | 30%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 36%
|
|========================== | 37%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 41%
|
|============================== | 42%
|
|=============================== | 44%
|
|================================ | 45%
|
|================================= | 47%
|
|================================== | 48%
|
|=================================== | 49%
|
|=================================== | 51%
|
|==================================== | 52%
|
|===================================== | 53%
|
|====================================== | 55%
|
|======================================= | 56%
|
|======================================== | 58%
|
|========================================= | 59%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 71%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|====================================================== | 77%
|
|======================================================= | 78%
|
|======================================================== | 79%
|
|========================================================= | 81%
|
|========================================================== | 82%
|
|========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 86%
|
|============================================================= | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|===================================================================== | 99%
|
|======================================================================| 100%
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.
|
| | 0%
Found 73 differentially methylated CpGs
Identifying functional CpG-gene pairs...
|
| | 0%
|
|== | 3%
|
|==== | 6%
|
|====== | 9%
|
|======== | 12%
|
|=========== | 15%
|
|============= | 18%
|
|=============== | 21%
|
|================= | 24%
|
|=================== | 27%
|
|===================== | 30%
|
|======================= | 33%
|
|========================= | 36%
|
|============================ | 39%
|
|============================== | 42%
|
|================================ | 45%
|
|================================== | 48%
|
|==================================== | 52%
|
|====================================== | 55%
|
|======================================== | 58%
|
|========================================== | 61%
|
|============================================= | 64%
|
|=============================================== | 67%
|
|================================================= | 70%
|
|=================================================== | 73%
|
|===================================================== | 76%
|
|======================================================= | 79%
|
|========================================================= | 82%
|
|=========================================================== | 85%
|
|============================================================== | 88%
|
|================================================================ | 91%
|
|================================================================== | 94%
|
|==================================================================== | 97%
|
|======================================================================| 100%
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
loading from cache
Returning distal probes: 160862
Found 7 CpGs associated with distal enhancers in the methylation dataset
Starting Beta mixture modeling.
Running Beta mixture model on 7 probes and on 17 samples.
|
| | 0%
Found 7 differentially methylated CpGs
Modeling the gene expression for enhancers...
Searching for the 20 near genes
Identifying gene position for each probe
Looking for differentially methylated enhancers associated with gene expression
|
| | 0%
|
|========== | 14%
|
|==================== | 29%
|
|============================== | 43%
|
|======================================== | 57%
|
|================================================== | 71%
|
|============================================================ | 86%
|
|======================================================================| 100%
Found 2 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
sesameData not installed.
Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
[1] "3 oncogenic mediator(s) out of 3 were found in the None evidence category"
|
| | 0%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%
|
|= | 1%
|
|= | 2%
|
| | 0%Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 65 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 65 ]
>
> proc.time()
user system elapsed
168.178 11.389 251.033
Moonlight2R.Rcheck/Moonlight2R-Ex.timings
| name | user | system | elapsed | |
| DMA | 0 | 0 | 0 | |
| FEA | 0.349 | 0.004 | 0.354 | |
| GLS | 2.891 | 1.197 | 6.772 | |
| GMA | 112.702 | 7.638 | 148.589 | |
| GRN | 0.055 | 0.000 | 0.054 | |
| GSEA | 1.546 | 0.092 | 2.314 | |
| LPA | 0.200 | 0.004 | 0.205 | |
| LiftMAF | 4.293 | 0.364 | 7.979 | |
| MAFtoCscape | 0.045 | 0.000 | 0.045 | |
| PRA | 0.172 | 0.004 | 0.176 | |
| PRAtoTibble | 0.039 | 0.004 | 0.042 | |
| RunCscape_somatic | 0 | 0 | 0 | |
| TFinfluence | 0.212 | 0.016 | 0.229 | |
| URA | 2.911 | 0.112 | 3.028 | |
| confidence | 0 | 0 | 0 | |
| getDataGEO | 2.673 | 0.354 | 13.137 | |
| loadMAVISp | 0.205 | 0.088 | 0.281 | |
| moonlight | 0.001 | 0.000 | 0.000 | |
| plotCircos | 1.080 | 0.159 | 1.243 | |
| plotDMA | 5.695 | 0.831 | 6.542 | |
| plotFEA | 0.388 | 0.036 | 0.425 | |
| plotGMA | 6.578 | 0.982 | 7.579 | |
| plotMetExp | 2.008 | 0.251 | 2.266 | |
| plotMoonlight | 3.496 | 0.239 | 3.754 | |
| plotMoonlightMet | 1.847 | 0.172 | 2.025 | |
| plotNetworkHive | 0.034 | 0.012 | 0.046 | |
| plotURA | 0.236 | 0.008 | 0.244 | |
| tabix_func | 0 | 0 | 0 | |