Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:14 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the methylumi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylumi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1167/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylumi 2.45.0 (landing page) Sean Davis
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: methylumi |
Version: 2.45.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylumi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings methylumi_2.45.0.tar.gz |
StartedAt: 2023-02-07 07:59:37 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 08:09:05 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 568.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: methylumi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylumi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings methylumi_2.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/methylumi.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘methylumi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylumi’ version ‘2.45.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'scales', 'reshape2', 'ggplot2', 'matrixStats', 'FDb.InfiniumMethylation.hg19', 'minfi' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘methylumi’ can be installed ... OK * checking installed package size ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: R 1.3Mb data 2.7Mb extdata 5.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’ A package should be listed in only one of these fields. * 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 ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’ ‘reshape2’ ‘scales’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘graphics’ All declared Imports should be used. Packages in Depends field not imported from: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’ ‘reshape2’ ‘scales’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Killed * checking Rd files ... NOTE prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples checkRd: (-1) extractBarcodeAndPosition.Rd:14: Escaped LaTeX specials: \_ \_ * 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 ... NOTE Killed * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘methylumi.Rnw’ using ‘UTF-8’... OK ‘methylumi450k.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘methylumi.Rnw’ using knitr Killed --- re-building ‘methylumi450k.Rnw’ using knitr Killed SUMMARY: processing the following files failed: ‘methylumi.Rnw’ ‘methylumi450k.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 8 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/methylumi.Rcheck/00check.log’ for details.
methylumi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL methylumi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘methylumi’ ... ** 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 (methylumi)
methylumi.Rcheck/methylumi-Ex.timings
name | user | system | elapsed | |
CpGs | 1.781 | 0.016 | 1.950 | |
MethyLumi-class | 0.423 | 0.025 | 0.522 | |
MethyLumiM-class | 0.001 | 0.000 | 0.013 | |
MethyLumiQC-class | 0.001 | 0.000 | 0.001 | |
MethyLumiSet-class | 0.001 | 0.000 | 0.001 | |
extractBarcodeAndPosition | 0.000 | 0.003 | 0.003 | |
getAssayDataNameSubstitutions | 0.002 | 0.000 | 0.002 | |
methylData-class | 0.001 | 0.000 | 0.000 | |
methylumIDAT | 0 | 0 | 0 | |
methylumiR | 0.283 | 0.008 | 0.297 | |
mldat | 0.057 | 0.007 | 0.122 | |
normalizeMethyLumiSet | 0.387 | 0.008 | 0.483 | |
plotSampleIntensities | 0.079 | 0.000 | 0.103 | |
qcplot | 0.264 | 0.028 | 0.347 | |
varFilter | 0.448 | 0.000 | 0.482 | |