Altuna Akalin
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_11 |
| Last Commit: a4a2fdf |
| Last Changed Date: 2020-05-20 12:13:42 -0400 (Wed, 20 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:56 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE methylKit PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1060/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methylKit 1.14.2 Altuna Akalin
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: methylKit |
| Version: 1.14.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylKit_1.14.2.tar.gz |
| StartedAt: 2020-10-17 02:56:16 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:04:51 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 515.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylKit.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylKit_1.14.2.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/methylKit.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.2’
* 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 ... NOTE
.CpG.dinuc.unify: no visible binding for global variable ‘coverage.x’
.CpG.dinuc.unify: no visible binding for global variable ‘coverage.y’
.CpG.dinuc.unify: no visible binding for global variable ‘numCs.x’
.CpG.dinuc.unify: no visible binding for global variable ‘numCs.y’
.CpG.dinuc.unify: no visible binding for global variable ‘numTs.x’
.CpG.dinuc.unify: no visible binding for global variable ‘numTs.y’
.diffMethPerChr: no visible binding for global variable ‘type’
.diffMethPerChr: no visible binding for global variable ‘meth.diff’
.diffMethPerChr: no visible global function definition for ‘.’
.diffMethPerChr: no visible binding for global variable ‘.N’
reconstruct,ANY-methylBaseDB : reconstr: no visible global function
definition for ‘read.delim’
Undefined global functions or variables:
. .N coverage.x coverage.y meth.diff numCs.x numCs.y numTs.x numTs.y
read.delim type
Consider adding
importFrom("utils", "read.delim")
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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/libs/methylKit.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘_srand48’, possibly from ‘srand48’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculateDiffMeth-methods 12.143 0.272 14.205
selectByOverlap-methods 5.185 0.112 6.245
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/methylKit.Rcheck/00check.log’
for details.
methylKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylKit ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘methylKit’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c methCall.cpp -o methCall.o clang++ -mmacosx-version-min=10.13 -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/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-methylKit/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (methylKit)
methylKit.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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
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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
paired sam.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
paired sam.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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: 189 | SKIPPED: 0 | WARNINGS: 344 | FAILED: 0 ]
>
> proc.time()
user system elapsed
110.719 2.312 122.998
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.049 | 0.005 | 0.069 | |
| adjustMethylC | 0.182 | 0.008 | 0.242 | |
| assocComp-methods | 0.037 | 0.005 | 0.047 | |
| bedgraph-methods | 0.040 | 0.007 | 0.054 | |
| calculateDiffMeth-methods | 12.143 | 0.272 | 14.205 | |
| calculateDiffMethDSS-methods | 0.932 | 0.009 | 1.115 | |
| clusterSamples-methods | 0.064 | 0.004 | 0.083 | |
| dataSim-methods | 0.030 | 0.003 | 0.040 | |
| diffMethPerChr-methods | 0.050 | 0.003 | 0.061 | |
| extract-methods | 0.047 | 0.003 | 0.062 | |
| filterByCoverage-methods | 0.149 | 0.008 | 0.183 | |
| getAssembly-methods | 0.018 | 0.003 | 0.020 | |
| getContext-methods | 0.017 | 0.003 | 0.023 | |
| getCorrelation-methods | 0.096 | 0.008 | 0.119 | |
| getCoverageStats-methods | 0.023 | 0.003 | 0.034 | |
| getDBPath-methods | 0.076 | 0.007 | 0.094 | |
| getData-methods | 0.032 | 0.005 | 0.042 | |
| getMethylDiff-methods | 0.029 | 0.003 | 0.040 | |
| getMethylationStats-methods | 0.035 | 0.004 | 0.042 | |
| getSampleID-methods | 0.018 | 0.003 | 0.024 | |
| getTreatment-methods | 0.018 | 0.002 | 0.023 | |
| makeMethylDB-methods | 0.000 | 0.000 | 0.001 | |
| methRead-methods | 0.386 | 0.032 | 0.505 | |
| methSeg | 0.001 | 0.001 | 0.000 | |
| methylBase-class | 0.036 | 0.003 | 0.047 | |
| methylBaseDB-class | 0.102 | 0.007 | 0.120 | |
| methylDiff-class | 0.042 | 0.003 | 0.051 | |
| methylDiffDB-class | 4.302 | 0.018 | 4.997 | |
| methylRaw-class | 0.105 | 0.007 | 0.126 | |
| methylRawDB-class | 0.125 | 0.009 | 0.152 | |
| methylRawList-class | 0.019 | 0.003 | 0.024 | |
| methylRawListDB-class | 0.204 | 0.019 | 0.254 | |
| normalizeCoverage-methods | 0.216 | 0.018 | 0.277 | |
| percMethylation-methods | 0.044 | 0.004 | 0.054 | |
| pool-methods | 0.026 | 0.003 | 0.031 | |
| processBismarkAln-methods | 0.137 | 0.012 | 0.187 | |
| readMethylDB-methods | 0.000 | 0.001 | 0.000 | |
| reconstruct-methods | 0.034 | 0.003 | 0.045 | |
| regionCounts | 0.591 | 0.004 | 0.703 | |
| removeComp-methods | 0.054 | 0.003 | 0.067 | |
| reorganize-methods | 0.203 | 0.005 | 0.252 | |
| select-methods | 0.136 | 0.011 | 0.174 | |
| selectByOverlap-methods | 5.185 | 0.112 | 6.245 | |
| show-methods | 0.048 | 0.004 | 0.057 | |
| tileMethylCounts-methods | 1.010 | 0.008 | 1.072 | |
| unite-methods | 0.173 | 0.005 | 0.188 | |