Lukas Chavez
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/MEDIPS |
| git_branch: RELEASE_3_20 |
| git_last_commit: 2de7e88 |
| git_last_commit_date: 2024-10-29 09:35:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1185/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MEDIPS 1.58.0 (landing page) Lukas Chavez
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the MEDIPS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEDIPS.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: MEDIPS |
| Version: 1.58.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MEDIPS_1.58.0.tar.gz |
| StartedAt: 2025-01-09 00:23:25 -0000 (Thu, 09 Jan 2025) |
| EndedAt: 2025-01-09 00:30:15 -0000 (Thu, 09 Jan 2025) |
| EllapsedTime: 409.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MEDIPS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MEDIPS_1.58.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MEDIPS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEDIPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEDIPS’ version ‘1.58.0’
* 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 ‘MEDIPS’ 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
MEDIPS.CpGenrich: no visible global function definition for ‘seqlevels’
MEDIPS.CpGenrich: no visible global function definition for
‘seqlengths’
MEDIPS.CpGenrich: no visible global function definition for
‘GRangesList’
MEDIPS.CpGenrich : <anonymous>: no visible global function definition
for ‘seqnames’
MEDIPS.CpGenrich: no visible global function definition for ‘new’
MEDIPS.addCNV: no visible global function definition for ‘seqnames’
MEDIPS.correlation: no visible global function definition for ‘pdf’
MEDIPS.correlation: no visible global function definition for ‘dev.off’
MEDIPS.couplingVector: no visible global function definition for ‘new’
MEDIPS.createROIset: no visible global function definition for
‘seqnames’
MEDIPS.createROIset: no visible global function definition for
‘seqlengths’
MEDIPS.createROIset: no visible global function definition for ‘new’
MEDIPS.createSet: no visible global function definition for ‘seqnames’
MEDIPS.createSet: no visible global function definition for
‘seqlengths’
MEDIPS.createSet: no visible global function definition for ‘seqlevels’
MEDIPS.createSet: no visible global function definition for ‘new’
MEDIPS.diffMeth: no visible global function definition for ‘p.adjust’
MEDIPS.exportWIG: no visible global function definition for ‘seqnames’
MEDIPS.mergeSets: no visible global function definition for ‘new’
MEDIPS.meth: no visible global function definition for ‘seqnames’
MEDIPS.plotCalibrationPlot: no visible global function definition for
‘seqnames’
MEDIPS.plotCalibrationPlot: no visible global function definition for
‘points’
MEDIPS.plotSeqCoverage: no visible global function definition for ‘pie’
MEDIPS.plotSeqCoverage: no visible global function definition for
‘hist’
MEDIPS.saturation: no visible global function definition for
‘seqlevels’
MEDIPS.saturation: no visible global function definition for
‘seqlengths’
MEDIPS.selectROIs: no visible global function definition for
‘elementMetadata<-’
MEDIPS.selectROIs: no visible global function definition for
‘elementMetadata’
MEDIPS.selectROIs: no visible global function definition for
‘findOverlaps’
MEDIPS.selectROIs: no visible global function definition for ‘values’
MEDIPS.selectROIs: no visible global function definition for ‘seqnames’
MEDIPS.seqCoverage: no visible global function definition for
‘seqlevels’
MEDIPS.seqCoverage: no visible global function definition for
‘seqlengths’
MEDIPS.setAnnotation: no visible global function definition for
‘findOverlaps’
MEDIPS.setAnnotation: no visible global function definition for
‘values’
getGRange: no visible global function definition for ‘qpois’
getGRange: no visible global function definition for ‘seqlengths’
getGRange: no visible global function definition for ‘countMatches’
getGRange: no visible global function definition for ‘strand<-’
getMObjectFromWIG: no visible global function definition for
‘seqlengths’
getMObjectFromWIG: no visible global function definition for ‘values’
getMObjectFromWIG: no visible global function definition for
‘runLength’
getMObjectFromWIG: no visible global function definition for ‘seqnames’
getMObjectFromWIG: no visible global function definition for ‘runValue’
getMObjectFromWIG: no visible global function definition for ‘new’
getPairedGRange: no visible global function definition for ‘sd’
getPairedGRange: no visible global function definition for ‘qpois’
getPairedGRange: no visible global function definition for ‘seqlengths’
getPairedGRange: no visible global function definition for
‘countMatches’
getPairedGRange: no visible global function definition for ‘strand<-’
matSd: no visible binding for global variable ‘sd’
matTtest: no visible binding for global variable ‘sd’
matTtest: no visible global function definition for ‘pt’
Undefined global functions or variables:
GRangesList countMatches dev.off elementMetadata elementMetadata<-
findOverlaps hist new p.adjust pdf pie points pt qpois runLength
runValue sd seqlengths seqlevels seqnames strand<- values
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "hist", "pie", "points")
importFrom("methods", "new")
importFrom("stats", "p.adjust", "pt", "qpois", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
MEDIPS.meth 42.050 1.492 43.624
MEDIPS.addCNV 31.214 0.555 31.825
MEDIPS.plotSaturation 11.256 0.148 11.425
MEDIPS.saturation 10.963 0.079 11.061
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.20-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.
MEDIPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MEDIPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’ * installing *source* package ‘MEDIPS’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’ ** testing if installed package can be loaded from final location No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’ ** testing if installed package keeps a record of temporary installation path * DONE (MEDIPS)
MEDIPS.Rcheck/MEDIPS-Ex.timings
| name | user | system | elapsed | |
| COUPLINGset-class | 0.001 | 0.000 | 0.002 | |
| MEDIPS.CpGenrich | 0.054 | 0.000 | 0.054 | |
| MEDIPS.addCNV | 31.214 | 0.555 | 31.825 | |
| MEDIPS.correlation | 1.966 | 0.000 | 1.969 | |
| MEDIPS.couplingVector | 3.345 | 0.052 | 3.403 | |
| MEDIPS.createROIset | 1.180 | 0.000 | 1.183 | |
| MEDIPS.createSet | 1.291 | 0.036 | 1.330 | |
| MEDIPS.exportWIG | 2.359 | 0.000 | 2.365 | |
| MEDIPS.getAnnotation | 0 | 0 | 0 | |
| MEDIPS.mergeFrames | 0.004 | 0.000 | 0.004 | |
| MEDIPS.mergeSets | 0.890 | 0.056 | 0.951 | |
| MEDIPS.meth | 42.050 | 1.492 | 43.624 | |
| MEDIPS.plotCalibrationPlot | 3.255 | 0.044 | 3.305 | |
| MEDIPS.plotSaturation | 11.256 | 0.148 | 11.425 | |
| MEDIPS.plotSeqCoverage | 3.057 | 0.100 | 3.162 | |
| MEDIPS.saturation | 10.963 | 0.079 | 11.061 | |
| MEDIPS.selectROIs | 1.471 | 0.004 | 1.477 | |
| MEDIPS.selectSig | 2.425 | 0.071 | 2.501 | |
| MEDIPS.seqCoverage | 3.016 | 0.028 | 3.048 | |
| MEDIPS.setAnnotation | 2.276 | 0.036 | 2.316 | |
| MEDIPSroiSet-class | 0 | 0 | 0 | |
| MEDIPSset-class | 0 | 0 | 0 | |