Altuna Akalin
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_7 |
| Last Commit: fd2779b |
| Last Changed Date: 2018-10-11 16:55:12 -0400 (Thu, 11 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:29:11 -0400 (Wed, 17 Oct 2018).
| Package 889/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methylKit 1.6.3 Altuna Akalin
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: methylKit |
| Version: 1.6.3 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methylKit_1.6.3.tar.gz |
| StartedAt: 2018-10-16 01:54:33 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:58:14 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 220.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylKit.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methylKit_1.6.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/methylKit.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylKit’ version ‘1.6.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methylKit’ 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 ... NOTE
Namespace in Imports field not imported from: ‘KernSmooth’
All declared Imports should be used.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calculateDiffMeth-methods 5.096 0.1 5.197
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/methylKit.Rcheck/00check.log’
for details.
methylKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL methylKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘methylKit’ ... ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c methCall.cpp -o methCall.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o -L/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/methylKit/libs ** 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 * DONE (methylKit)
methylKit.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> library(testthat)
> library(methylKit)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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, colMeans, colSums, colnames,
dirname, 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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
>
>
> test_check("methylKit")
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
paired sam.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
paired sam.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.bismark_single_end.sorted.bam
using htslib.
Conversion Statistics:
total otherC considered (>95% C+T): 20
average conversion rate = 95.184207585947
total otherC considered (Forward) (>95% C+T): 8
average conversion rate (Forward) = 97.528594771242
total otherC considered (Reverse) (>95% C+T): 12
average conversion rate (Reverse) = 93.62128279575
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/ctrl.bismark_paired_end.sorted.bam
using htslib.
Conversion Statistics:
total otherC considered (>95% C+T): 4
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 4
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: ctrl1
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/home/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Using internal DSS code...
Using internal DSS code...
══ testthat results ═══════════════════════════════════════════════════════════
OK: 423 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
33.572 0.384 34.018
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.020 | 0.000 | 0.019 | |
| adjustMethylC | 0.080 | 0.012 | 0.107 | |
| assocComp-methods | 0.016 | 0.000 | 0.013 | |
| bedgraph-methods | 0.024 | 0.000 | 0.025 | |
| calculateDiffMeth-methods | 5.096 | 0.100 | 5.197 | |
| calculateDiffMethDSS-methods | 0.368 | 0.000 | 0.369 | |
| clusterSamples-methods | 0.024 | 0.000 | 0.025 | |
| dataSim-methods | 0.012 | 0.000 | 0.014 | |
| diffMethPerChr-methods | 0.008 | 0.004 | 0.015 | |
| extract-methods | 0.016 | 0.000 | 0.018 | |
| filterByCoverage-methods | 0.048 | 0.008 | 0.055 | |
| getAssembly-methods | 0.004 | 0.000 | 0.004 | |
| getContext-methods | 0.004 | 0.000 | 0.005 | |
| getCorrelation-methods | 0.072 | 0.000 | 0.073 | |
| getCoverageStats-methods | 0.008 | 0.000 | 0.008 | |
| getDBPath-methods | 0.040 | 0.000 | 0.039 | |
| getData-methods | 0.008 | 0.000 | 0.010 | |
| getMethylDiff-methods | 0.004 | 0.004 | 0.011 | |
| getMethylationStats-methods | 0.012 | 0.000 | 0.012 | |
| getSampleID-methods | 0.004 | 0.000 | 0.005 | |
| getTreatment-methods | 0.004 | 0.000 | 0.004 | |
| makeMethylDB-methods | 0.000 | 0.000 | 0.001 | |
| methRead-methods | 0.168 | 0.004 | 0.203 | |
| methSeg | 0.004 | 0.000 | 0.000 | |
| methylBase-class | 0.012 | 0.000 | 0.011 | |
| methylBaseDB-class | 0.060 | 0.000 | 0.059 | |
| methylDiff-class | 0.012 | 0.000 | 0.013 | |
| methylDiffDB-class | 1.852 | 0.000 | 1.850 | |
| methylRaw-class | 0.040 | 0.000 | 0.041 | |
| methylRawDB-class | 0.064 | 0.000 | 0.062 | |
| methylRawList-class | 0.004 | 0.000 | 0.005 | |
| methylRawListDB-class | 0.100 | 0.000 | 0.101 | |
| normalizeCoverage-methods | 0.144 | 0.000 | 0.143 | |
| percMethylation-methods | 0.016 | 0.000 | 0.014 | |
| pool-methods | 0.008 | 0.000 | 0.008 | |
| processBismarkAln-methods | 0.056 | 0.000 | 0.067 | |
| reconstruct-methods | 0.012 | 0.000 | 0.012 | |
| regionCounts | 0.200 | 0.000 | 0.202 | |
| removeComp-methods | 0.024 | 0.000 | 0.021 | |
| reorganize-methods | 0.220 | 0.004 | 0.223 | |
| select-methods | 0.084 | 0.004 | 0.111 | |
| selectByOverlap-methods | 2.568 | 0.012 | 2.582 | |
| show-methods | 0.016 | 0.000 | 0.018 | |
| tileMethylCounts-methods | 0.356 | 0.000 | 0.359 | |
| unite-methods | 0.080 | 0.000 | 0.081 | |