Tim Peters
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/DMRcate |
| Branch: RELEASE_3_10 |
| Last Commit: 705da73 |
| Last Changed Date: 2020-01-09 18:51:43 -0400 (Thu, 09 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:22:38 -0400 (Wed, 15 Apr 2020).
| Package 470/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DMRcate 2.0.7 Tim Peters
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DMRcate |
| Version: 2.0.7 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcate.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DMRcate_2.0.7.tar.gz |
| StartedAt: 2020-04-15 02:44:12 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:19:49 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 2137.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DMRcate.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcate.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DMRcate_2.0.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/DMRcate.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRcate/DESCRIPTION' ... OK
* this is package 'DMRcate' version '2.0.7'
* 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 'DMRcate' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/DMRcate.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'DMRcate-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DMR.plot
> ### Title: Plotting DMRs
> ### Aliases: DMR.plot plot
>
> ### ** Examples
>
> library(ExperimentHub)
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: 'AnnotationHub'
The following object is masked from 'package:Biobase':
cache
> library(limma)
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
> eh <- ExperimentHub()
snapshotDate(): 2019-10-22
> FlowSorted.Blood.EPIC <- eh[["EH1136"]]
see ?FlowSorted.Blood.EPIC and browseVignettes('FlowSorted.Blood.EPIC') for documentation
loading from cache
> tcell <- FlowSorted.Blood.EPIC[,colData(FlowSorted.Blood.EPIC)$CD4T==100 |
+ colData(FlowSorted.Blood.EPIC)$CD8T==100]
> detP <- detectionP(tcell)
Loading required package: IlluminaHumanMethylationEPICmanifest
> remove <- apply(detP, 1, function (x) any(x > 0.01))
> tcell <- tcell[!remove,]
> tcell <- preprocessFunnorm(tcell)
[preprocessFunnorm] Background and dye bias correction with noob
Error: cannot allocate vector of size 85.7 Mb
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DMR.plot 210.58 14.81 253.41
DMRcate-package 186.27 12.55 200.01
extractRanges 163.14 11.24 176.06
rmSNPandCH 160.42 11.42 172.88
dmrcate 146.84 12.90 160.96
cpg.annotate 137.91 12.94 152.39
sequencing.annotate 68.15 6.44 74.86
changeFDR 58.55 4.39 224.62
* 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 ERROR, 1 WARNING
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/DMRcate.Rcheck/00check.log'
for details.
DMRcate.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/DMRcate_2.0.7.tar.gz && rm -rf DMRcate.buildbin-libdir && mkdir DMRcate.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRcate.buildbin-libdir DMRcate_2.0.7.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL DMRcate_2.0.7.zip && rm DMRcate_2.0.7.tar.gz DMRcate_2.0.7.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 63268 100 63268 0 0 2086k 0 --:--:-- --:--:-- --:--:-- 2376k
install for i386
* installing *source* package 'DMRcate' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** help
*** installing help indices
converting help for package 'DMRcate'
finding HTML links ... done
CpGannotated-class html
DMR.plot html
DMRcate-internal html
DMRcate-package html
DMResults-class html
changeFDR html
cpg.annotate html
dmrcate html
extractRanges html
rmSNPandCH html
sequencing.annotate html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'DMRcate' ...
** testing if installed package can be loaded
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
* MD5 sums
packaged installation of 'DMRcate' as DMRcate_2.0.7.zip
* DONE (DMRcate)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'DMRcate' successfully unpacked and MD5 sums checked
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DMRcate.Rcheck/examples_i386/DMRcate-Ex.timings
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DMRcate.Rcheck/examples_x64/DMRcate-Ex.timings
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