Altuna Akalin
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_6 |
| Last Commit: dd0dd4c |
| Last Changed Date: 2018-01-22 10:25:01 -0400 (Mon, 22 Jan 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:43:16 -0400 (Thu, 12 Apr 2018).
| Package 839/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methylKit 1.4.1 Altuna Akalin
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: methylKit |
| Version: 1.4.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylKit_1.4.1.tar.gz |
| StartedAt: 2018-04-12 06:16:43 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 06:21:55 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 312.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylKit.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylKit_1.4.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.1’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calculateDiffMeth-methods 8.198 0.069 8.287
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/00check.log’
for details.
methylKit.Rcheck/00install.out
* installing *source* package ‘methylKit’ ... ** libs clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c methCall.cpp -o methCall.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/lib/libhts.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] installing to /Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/libs ** R ** data ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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
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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
paired sam.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
paired sam.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/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
48.593 1.876 46.273
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.028 | 0.006 | 0.034 | |
| adjustMethylC | 0.499 | 0.024 | 0.511 | |
| assocComp-methods | 0.029 | 0.006 | 0.019 | |
| bedgraph-methods | 0.043 | 0.008 | 0.035 | |
| calculateDiffMeth-methods | 8.198 | 0.069 | 8.287 | |
| calculateDiffMethDSS-methods | 0.816 | 0.005 | 0.839 | |
| clusterSamples-methods | 0.039 | 0.003 | 0.043 | |
| dataSim-methods | 0.104 | 0.001 | 0.106 | |
| diffMethPerChr-methods | 0.019 | 0.002 | 0.021 | |
| extract-methods | 0.020 | 0.001 | 0.021 | |
| filterByCoverage-methods | 0.097 | 0.003 | 0.100 | |
| getAssembly-methods | 0.005 | 0.002 | 0.006 | |
| getContext-methods | 0.003 | 0.001 | 0.005 | |
| getCorrelation-methods | 0.447 | 0.088 | 0.265 | |
| getCoverageStats-methods | 0.025 | 0.009 | 0.011 | |
| getDBPath-methods | 0.161 | 0.049 | 0.071 | |
| getData-methods | 0.037 | 0.014 | 0.018 | |
| getMethylDiff-methods | 0.033 | 0.011 | 0.015 | |
| getMethylationStats-methods | 0.056 | 0.016 | 0.024 | |
| getSampleID-methods | 0.014 | 0.005 | 0.007 | |
| getTreatment-methods | 0.014 | 0.005 | 0.008 | |
| makeMethylDB-methods | 0.002 | 0.001 | 0.001 | |
| methRead-methods | 0.354 | 0.050 | 0.282 | |
| methSeg | 0.001 | 0.000 | 0.001 | |
| methylBase-class | 0.161 | 0.002 | 0.166 | |
| methylBaseDB-class | 0.113 | 0.018 | 0.072 | |
| methylDiff-class | 0.026 | 0.005 | 0.017 | |
| methylDiffDB-class | 2.925 | 0.041 | 2.927 | |
| methylRaw-class | 0.057 | 0.003 | 0.059 | |
| methylRawDB-class | 0.081 | 0.004 | 0.084 | |
| methylRawList-class | 0.005 | 0.001 | 0.007 | |
| methylRawListDB-class | 0.124 | 0.007 | 0.139 | |
| normalizeCoverage-methods | 0.167 | 0.007 | 0.175 | |
| percMethylation-methods | 0.018 | 0.001 | 0.023 | |
| pool-methods | 0.077 | 0.001 | 0.091 | |
| processBismarkAln-methods | 0.080 | 0.006 | 0.095 | |
| reconstruct-methods | 0.015 | 0.001 | 0.017 | |
| regionCounts | 1.853 | 0.096 | 1.721 | |
| removeComp-methods | 0.115 | 0.014 | 0.091 | |
| reorganize-methods | 0.547 | 0.067 | 0.375 | |
| select-methods | 0.137 | 0.028 | 0.076 | |
| selectByOverlap-methods | 3.110 | 0.079 | 3.143 | |
| show-methods | 0.017 | 0.001 | 0.019 | |
| tileMethylCounts-methods | 1.072 | 0.109 | 0.792 | |
| unite-methods | 0.174 | 0.027 | 0.101 | |