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 11:55:07 -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: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings methylKit_1.14.2.tar.gz |
| StartedAt: 2020-10-17 03:05:43 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:12:12 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 389.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylKit.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings methylKit_1.14.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/methylKit.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.2’
* 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 ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
R 1.4Mb
libs 4.1Mb
* 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 ‘/home/biocbuild/bbs-3.11-bioc/R/library/methylKit/libs/methylKit.so’:
Found ‘__printf_chk’, possibly from ‘printf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘putchar’, possibly from ‘putchar’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘srand48’, possibly from ‘srand48’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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 7.22 0.12 7.34
* 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/methylKit.Rcheck/00check.log’
for details.
methylKit.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL methylKit
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c methCall.cpp -o methCall.o
methCall.cpp: In function ‘int process_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)’:
methCall.cpp:1220:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1219:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1218:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int)’:
methCall.cpp:678:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:677:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:676:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int)’:
methCall.cpp:997:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:996:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:995:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/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-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, 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:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
paired sam.
Trying to process:
/home/biocbuild/bbs-3.11-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-3.11-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
paired sam.
Trying to process:
/home/biocbuild/bbs-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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-3.11-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: 189 | SKIPPED: 0 | WARNINGS: 344 | FAILED: 0 ]
>
> proc.time()
user system elapsed
103.896 0.990 106.235
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.039 | 0.000 | 0.038 | |
| adjustMethylC | 0.151 | 0.007 | 0.166 | |
| assocComp-methods | 0.032 | 0.000 | 0.032 | |
| bedgraph-methods | 0.038 | 0.000 | 0.038 | |
| calculateDiffMeth-methods | 7.22 | 0.12 | 7.34 | |
| calculateDiffMethDSS-methods | 0.435 | 0.004 | 0.439 | |
| clusterSamples-methods | 0.031 | 0.000 | 0.031 | |
| dataSim-methods | 0.017 | 0.000 | 0.016 | |
| diffMethPerChr-methods | 0.066 | 0.004 | 0.032 | |
| extract-methods | 0.026 | 0.000 | 0.027 | |
| filterByCoverage-methods | 0.077 | 0.004 | 0.081 | |
| getAssembly-methods | 0.009 | 0.000 | 0.009 | |
| getContext-methods | 0.009 | 0.000 | 0.009 | |
| getCorrelation-methods | 0.072 | 0.000 | 0.057 | |
| getCoverageStats-methods | 0.013 | 0.000 | 0.013 | |
| getDBPath-methods | 0.063 | 0.000 | 0.048 | |
| getData-methods | 0.016 | 0.000 | 0.016 | |
| getMethylDiff-methods | 0.015 | 0.000 | 0.015 | |
| getMethylationStats-methods | 0.021 | 0.000 | 0.021 | |
| getSampleID-methods | 0.01 | 0.00 | 0.01 | |
| getTreatment-methods | 0.01 | 0.00 | 0.01 | |
| makeMethylDB-methods | 0 | 0 | 0 | |
| methRead-methods | 0.234 | 0.003 | 0.256 | |
| methSeg | 0 | 0 | 0 | |
| methylBase-class | 0.018 | 0.000 | 0.019 | |
| methylBaseDB-class | 0.072 | 0.001 | 0.058 | |
| methylDiff-class | 0.024 | 0.000 | 0.024 | |
| methylDiffDB-class | 2.163 | 0.000 | 2.164 | |
| methylRaw-class | 0.053 | 0.004 | 0.057 | |
| methylRawDB-class | 0.076 | 0.000 | 0.071 | |
| methylRawList-class | 0.010 | 0.000 | 0.009 | |
| methylRawListDB-class | 0.121 | 0.003 | 0.125 | |
| normalizeCoverage-methods | 0.129 | 0.004 | 0.133 | |
| percMethylation-methods | 0.023 | 0.000 | 0.022 | |
| pool-methods | 0.014 | 0.000 | 0.013 | |
| processBismarkAln-methods | 0.074 | 0.000 | 0.085 | |
| readMethylDB-methods | 0.000 | 0.000 | 0.001 | |
| reconstruct-methods | 0.017 | 0.001 | 0.017 | |
| regionCounts | 0.348 | 0.003 | 0.351 | |
| removeComp-methods | 0.045 | 0.000 | 0.045 | |
| reorganize-methods | 0.153 | 0.000 | 0.117 | |
| select-methods | 0.091 | 0.000 | 0.077 | |
| selectByOverlap-methods | 2.908 | 0.016 | 2.914 | |
| show-methods | 0.027 | 0.000 | 0.026 | |
| tileMethylCounts-methods | 0.581 | 0.001 | 0.570 | |
| unite-methods | 0.155 | 0.004 | 0.107 | |