Lukas Chavez
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MEDIPS |
| git_branch: RELEASE_3_17 |
| git_last_commit: 435df87 |
| git_last_commit_date: 2023-04-25 10:18:20 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:18 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1152/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MEDIPS 1.52.0 (landing page) Lukas Chavez
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: MEDIPS |
| Version: 1.52.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDIPS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MEDIPS_1.52.0.tar.gz |
| StartedAt: 2023-10-16 03:46:36 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 03:52:28 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 351.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MEDIPS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDIPS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MEDIPS_1.52.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/MEDIPS.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.52.0'
* 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 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 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MEDIPS.meth 39.60 1.00 40.64
MEDIPS.addCNV 21.20 0.38 35.15
MEDIPS.plotSaturation 5.45 0.28 5.73
MEDIPS.saturation 5.41 0.30 5.70
MEDIPS.plotSeqCoverage 5.17 0.09 5.27
MEDIPS.couplingVector 5.11 0.03 5.14
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
'F:/biocbuild/bbs-3.17-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.
MEDIPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MEDIPS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 | 0 | 0 | |
| MEDIPS.CpGenrich | 0.03 | 0.01 | 0.06 | |
| MEDIPS.addCNV | 21.20 | 0.38 | 35.15 | |
| MEDIPS.correlation | 1.45 | 0.03 | 1.64 | |
| MEDIPS.couplingVector | 5.11 | 0.03 | 5.14 | |
| MEDIPS.createROIset | 1.23 | 0.06 | 1.31 | |
| MEDIPS.createSet | 1.24 | 0.03 | 1.27 | |
| MEDIPS.exportWIG | 2.27 | 0.05 | 2.32 | |
| MEDIPS.getAnnotation | 0 | 0 | 0 | |
| MEDIPS.mergeFrames | 0 | 0 | 0 | |
| MEDIPS.mergeSets | 0.79 | 0.02 | 0.88 | |
| MEDIPS.meth | 39.60 | 1.00 | 40.64 | |
| MEDIPS.plotCalibrationPlot | 3.25 | 0.08 | 3.33 | |
| MEDIPS.plotSaturation | 5.45 | 0.28 | 5.73 | |
| MEDIPS.plotSeqCoverage | 5.17 | 0.09 | 5.27 | |
| MEDIPS.saturation | 5.41 | 0.30 | 5.70 | |
| MEDIPS.selectROIs | 1.27 | 0.03 | 1.30 | |
| MEDIPS.selectSig | 2.07 | 0.12 | 2.20 | |
| MEDIPS.seqCoverage | 4.85 | 0.08 | 4.92 | |
| MEDIPS.setAnnotation | 2.01 | 0.13 | 2.14 | |
| MEDIPSroiSet-class | 0 | 0 | 0 | |
| MEDIPSset-class | 0.00 | 0.01 | 0.02 | |