Tim Peters
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/DMRcate |
| Branch: RELEASE_3_9 |
| Last Commit: 2925c30 |
| Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:29:16 -0400 (Wed, 16 Oct 2019).
| Package 448/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DMRcate 1.20.0 Tim Peters
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DMRcate |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcate.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DMRcate_1.20.0.tar.gz |
| StartedAt: 2019-10-16 03:18:08 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:33:21 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 912.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DMRcate.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcate.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DMRcate_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DMRcate.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.20.0'
* 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 'DMRcate' 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
* 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: DMRcate-package
> ### Title: DMR calling from bisulphite sequencing and Illumina array data
> ### Aliases: DMRcate-package DMRcate
>
> ### ** Examples
>
> data(dmrcatedata)
> myMs <- logit2(myBetas)
> myMs.noSNPs <- rmSNPandCH(myMs, dist=2, mafcut=0.05)
> patient <- factor(sub("-.*", "", colnames(myMs)))
> type <- factor(sub(".*-", "", colnames(myMs)))
> design <- model.matrix(~patient + type)
> myannotation <- cpg.annotate("array", myMs.noSNPs, what="M", arraytype = "450K",
+ analysis.type="differential", design=design, coef=39)
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
> dmrcoutput <- dmrcate(myannotation, lambda=1000, C=2)
Fitting chr20...
Demarcating regions...
Done!
> results.ranges <- extractRanges(dmrcoutput, genome = "hg19")
> groups <- c(Tumour="magenta", Normal="forestgreen")
> cols <- groups[as.character(type)]
> samps <- c(1:6, 38+(1:6))
> DMR.plot(ranges=results.ranges, dmr=1, CpGs=myBetas, phen.col=cols, genome="hg19", samps=samps)
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Failed with error: 'cannot allocate vector of size 510.7 Mb'
Error in makeGenomicRatioSetFromMatrix(CpGs, array = "IlluminaHumanMethylationEPIC", :
cannot load annotation package IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Calls: DMR.plot -> makeGenomicRatioSetFromMatrix
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DMRcate-package 154.17 4.59 175.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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
See
'C:/Users/biocbuild/bbs-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DMRcate_1.20.0.tar.gz && rm -rf DMRcate.buildbin-libdir && mkdir DMRcate.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRcate.buildbin-libdir DMRcate_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DMRcate_1.20.0.zip && rm DMRcate_1.20.0.tar.gz DMRcate_1.20.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'DMRcate' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DMRcate'
finding HTML links ... done
DMR.plot html
DMRcate-internal html
DMRcate-package html
cpg.annotate html
dmrcate html
extractRanges html
rmSNPandCH html
** 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
install for x64
* installing *source* package 'DMRcate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRcate' as DMRcate_1.20.0.zip
* DONE (DMRcate)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DMRcate' successfully unpacked and MD5 sums checked
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DMRcate.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("DMRcate")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.1 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'bsseq'
The following object is masked from 'package:minfi':
getMeth
RUNIT TEST PROTOCOL -- Wed Oct 16 03:32:08 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
DMRcate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
>
>
>
>
> proc.time()
user system elapsed
59.17 3.95 63.25
|
DMRcate.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("DMRcate")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.1 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'bsseq'
The following object is masked from 'package:minfi':
getMeth
RUNIT TEST PROTOCOL -- Wed Oct 16 03:33:05 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
DMRcate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
>
>
>
>
> proc.time()
user system elapsed
54.82 1.65 56.53
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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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