Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:37 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the MEDIPS package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1109/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MEDIPS 1.51.0 (landing page) Lukas Chavez
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: MEDIPS |
Version: 1.51.0 |
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_1.51.0.tar.gz |
StartedAt: 2022-12-29 01:07:44 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 01:12:38 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 294.5 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_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MEDIPS.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server 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 '1.51.0' * 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 38.23 0.97 39.27 MEDIPS.addCNV 19.63 0.29 20.23 * 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-rtools43/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 | 0.00 | 0.08 | |
MEDIPS.addCNV | 19.63 | 0.29 | 20.23 | |
MEDIPS.correlation | 1.06 | 0.08 | 1.14 | |
MEDIPS.couplingVector | 4.30 | 0.08 | 4.39 | |
MEDIPS.createROIset | 0.94 | 0.01 | 0.95 | |
MEDIPS.createSet | 0.92 | 0.07 | 0.99 | |
MEDIPS.exportWIG | 1.89 | 0.08 | 1.97 | |
MEDIPS.getAnnotation | 0 | 0 | 0 | |
MEDIPS.mergeFrames | 0.02 | 0.00 | 0.01 | |
MEDIPS.mergeSets | 0.63 | 0.01 | 0.66 | |
MEDIPS.meth | 38.23 | 0.97 | 39.27 | |
MEDIPS.plotCalibrationPlot | 2.89 | 0.08 | 2.96 | |
MEDIPS.plotSaturation | 4.77 | 0.20 | 4.97 | |
MEDIPS.plotSeqCoverage | 4.14 | 0.08 | 4.22 | |
MEDIPS.saturation | 4.42 | 0.23 | 4.66 | |
MEDIPS.selectROIs | 1.40 | 0.02 | 1.42 | |
MEDIPS.selectSig | 1.85 | 0.05 | 1.89 | |
MEDIPS.seqCoverage | 4.36 | 0.06 | 4.42 | |
MEDIPS.setAnnotation | 1.81 | 0.09 | 1.91 | |
MEDIPSroiSet-class | 0 | 0 | 0 | |
MEDIPSset-class | 0 | 0 | 0 | |