Nicolae Radu Zabet
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/DMRcaller |
| Branch: RELEASE_3_6 |
| Last Commit: be6aed1 |
| Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:02 -0400 (Thu, 12 Apr 2018).
| Package 375/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DMRcaller 1.10.0 Nicolae Radu Zabet
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: DMRcaller |
| Version: 1.10.0 |
| Command: rm -rf DMRcaller.buildbin-libdir DMRcaller.Rcheck && mkdir DMRcaller.buildbin-libdir DMRcaller.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcaller.buildbin-libdir DMRcaller_1.10.0.tar.gz >DMRcaller.Rcheck\00install.out 2>&1 && cp DMRcaller.Rcheck\00install.out DMRcaller-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRcaller.buildbin-libdir --install="check:DMRcaller-install.out" --force-multiarch --no-vignettes --timings DMRcaller_1.10.0.tar.gz |
| StartedAt: 2018-04-11 23:34:12 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:37:54 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 222.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DMRcaller.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf DMRcaller.buildbin-libdir DMRcaller.Rcheck && mkdir DMRcaller.buildbin-libdir DMRcaller.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcaller.buildbin-libdir DMRcaller_1.10.0.tar.gz >DMRcaller.Rcheck\00install.out 2>&1 && cp DMRcaller.Rcheck\00install.out DMRcaller-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRcaller.buildbin-libdir --install="check:DMRcaller-install.out" --force-multiarch --no-vignettes --timings DMRcaller_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DMRcaller.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRcaller/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DMRcaller' version '1.10.0'
* 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 'DMRcaller' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
.computeAdjuestedPValues: no visible global function definition for
'p.adjust'
.computeaAjustedPValuesInDMRs: no visible global function definition
for 'p.adjust'
.fisherTestPValue: no visible global function definition for
'fisher.test'
.isColor: no visible global function definition for 'colors'
.plotGeneticElements: no visible global function definition for 'text'
.plotGeneticElements: no visible global function definition for 'lines'
.plotGeneticElements: no visible global function definition for
'segments'
.plotGeneticElements: no visible global function definition for 'rect'
.scoreTest: no visible global function definition for 'pnorm'
plotLocalMethylationProfile: no visible global function definition for
'colorRampPalette'
plotLocalMethylationProfile: no visible global function definition for
'plot'
plotLocalMethylationProfile: no visible global function definition for
'axis'
plotLocalMethylationProfile: no visible global function definition for
'points'
plotLocalMethylationProfile: no visible global function definition for
'legend'
plotLocalMethylationProfile: no visible global function definition for
'segments'
plotLocalMethylationProfile: no visible global function definition for
'rect'
plotLocalMethylationProfile: no visible global function definition for
'text'
plotLocalMethylationProfile: no visible global function definition for
'par'
plotLocalMethylationProfile: no visible global function definition for
'mtext'
plotMethylationDataCoverage: no visible global function definition for
'rainbow'
plotMethylationDataCoverage: no visible global function definition for
'par'
plotMethylationDataCoverage: no visible global function definition for
'plot'
plotMethylationDataCoverage: no visible global function definition for
'lines'
plotMethylationDataCoverage: no visible global function definition for
'axis'
plotMethylationDataCoverage: no visible global function definition for
'legend'
plotMethylationDataCoverage: no visible global function definition for
'mtext'
plotMethylationProfile: no visible global function definition for
'rainbow'
plotMethylationProfile: no visible global function definition for
'plot'
plotMethylationProfile: no visible global function definition for
'lines'
plotMethylationProfile: no visible global function definition for
'legend'
plotMethylationProfile: no visible global function definition for
'mtext'
plotMethylationProfile: no visible global function definition for
'axis'
plotMethylationProfileFromData: no visible global function definition
for 'rainbow'
plotMethylationProfileFromData: no visible global function definition
for 'par'
plotOverlapProfile: no visible global function definition for
'colorRampPalette'
plotOverlapProfile: no visible global function definition for 'par'
plotOverlapProfile: no visible global function definition for 'plot'
plotOverlapProfile: no visible global function definition for 'rect'
plotOverlapProfile: no visible global function definition for 'mtext'
plotOverlapProfile: no visible global function definition for 'text'
saveBismark: no visible global function definition for 'write.table'
Undefined global functions or variables:
axis colorRampPalette colors fisher.test legend lines mtext p.adjust
par plot pnorm points rainbow rect segments text write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "colors", "rainbow")
importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
"plot", "points", "rect", "segments", "text")
importFrom("stats", "fisher.test", "p.adjust", "pnorm")
importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readBismarkPool 7.91 0.29 8.2
computeDMRs 5.11 0.10 5.2
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readBismarkPool 7.55 0.33 7.87
computeDMRs 5.82 0.12 5.94
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/DMRcaller.Rcheck/00check.log'
for details.
DMRcaller.Rcheck/00install.out
install for i386
* installing *source* package 'DMRcaller' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'DMRcaller'
finding HTML links ... done
DMRcaller html
finding level-2 HTML links ... done
DMRsNoiseFilterCG html
GEs html
analyseReadsInsideRegionsForCondition html
computeDMRs html
computeMethylationDataCoverage html
computeMethylationProfile html
computeOverlapProfile html
filterDMRs html
getWholeChromosomes html
mergeDMRsIteratively html
methylationDataList html
plotLocalMethylationProfile html
plotMethylationDataCoverage html
plotMethylationProfile html
plotMethylationProfileFromData html
plotOverlapProfile html
poolMethylationDatasets html
poolTwoMethylationDatasets html
readBismark html
readBismarkPool html
saveBismark html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DMRcaller' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRcaller' as DMRcaller_1.10.0.zip
* DONE (DMRcaller)
In R CMD INSTALL
In R CMD INSTALL
|
DMRcaller.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("DMRcaller")
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Calculating interpolations...
Identifying DMRs...
Analysed reads inside DMRs
Merge DMRs iteratively
Filter DMRs
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Selecting data...
Identifying DMRs...
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Count inside each bin...
Filter the bins...
Identifying DMRs...
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs
Parameters checking ...
Merge DMRs iteratively ...
RUNIT TEST PROTOCOL -- Wed Apr 11 23:37:39 2018
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
DMRcaller RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
Warning message:
In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) :
'x' has been rounded to integer: Mean relative difference: 0.002857143
>
> proc.time()
user system elapsed
5.85 0.18 6.03
|
DMRcaller.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("DMRcaller")
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Calculating interpolations...
Identifying DMRs...
Analysed reads inside DMRs
Merge DMRs iteratively
Filter DMRs
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Selecting data...
Identifying DMRs...
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Count inside each bin...
Filter the bins...
Identifying DMRs...
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs
Parameters checking ...
Merge DMRs iteratively ...
RUNIT TEST PROTOCOL -- Wed Apr 11 23:37:47 2018
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
DMRcaller RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
Warning message:
In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) :
'x' has been rounded to integer: Mean relative difference: 0.002857143
>
> proc.time()
user system elapsed
7.96 0.14 8.09
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DMRcaller.Rcheck/examples_i386/DMRcaller-Ex.timings
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DMRcaller.Rcheck/examples_x64/DMRcaller-Ex.timings
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