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This page was generated on 2023-04-12 11:05:10 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for methylKit on nebbiolo2


To the developers/maintainers of the methylKit package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylKit.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1174/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.24.0  (landing page)
Altuna Akalin , Alexander Gosdschan
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/methylKit
git_branch: RELEASE_3_16
git_last_commit: 9870e27
git_last_commit_date: 2022-11-01 11:14:04 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: methylKit
Version: 1.24.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings methylKit_1.24.0.tar.gz
StartedAt: 2023-04-10 21:52:59 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:59:17 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 378.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: methylKit.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings methylKit_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/methylKit.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘methylKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylKit’ version ‘1.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methylKit’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   7.4Mb
* 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 loading without being on the library search path ... 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 ... WARNING
Undocumented arguments in documentation object 'methylRawList-class'
  ‘...’ ‘treatment’

Undocumented arguments in documentation object 'methylRawListDB-class'
  ‘...’ ‘treatment’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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-3.16-bioc/R/site-library/methylKit/libs/methylKit.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (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 5.117  0.152   5.269
* 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 ...
  ‘methylKit.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/methylKit.Rcheck/00check.log’
for details.



Installation output

methylKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL methylKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c methCall.cpp -o methCall.o
methCall.cpp: In function ‘int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int, size_t&)’:
methCall.cpp:687:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  687 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:686:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  686 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:685:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  685 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)’:
methCall.cpp:1014:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1014 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1013:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1013 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1012:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1012 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, size_t&)’:
methCall.cpp:1244:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1244 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1243:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1243 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1242:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1242 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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)

Tests output

methylKit.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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

Attaching package: 'BiocGenerics'

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, aperm, 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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> 
> 
> test_check("methylKit")
Using internal DSS code... 
Using internal DSS code... 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 238 ]
> 
> proc.time()
   user  system elapsed 
 76.035   2.129  76.851 

Example timings

methylKit.Rcheck/methylKit-Ex.timings

nameusersystemelapsed
PCASamples-methods0.0260.0000.026
adjustMethylC0.1560.0010.141
assocComp-methods0.0190.0000.018
bedgraph-methods0.0240.0040.027
calculateDiffMeth-methods5.1170.1525.269
calculateDiffMethDSS-methods0.4390.0360.474
clusterSamples-methods0.0260.0080.034
dataSim-methods0.0170.0000.017
diffMethPerChr-methods0.0340.0040.030
extract-methods0.0290.0000.029
filterByCoverage-methods0.1540.0000.154
getAssembly-methods0.0080.0000.009
getContext-methods0.0080.0000.009
getCorrelation-methods0.0690.0000.052
getCoverageStats-methods0.0130.0000.012
getDBPath-methods0.0570.0000.042
getData-methods0.0150.0000.016
getMethylDiff-methods0.0130.0000.014
getMethylationStats-methods0.0180.0000.018
getSampleID-methods0.0080.0000.009
getTreatment-methods0.0080.0000.009
makeMethylDB-methods000
methRead-methods0.2140.0040.219
methSeg000
methylBase-class0.0190.0000.019
methylBaseDB-class0.0740.0000.057
methylDiff-class0.0210.0000.022
methylDiffDB-class1.7540.0121.767
methylRaw-class0.0590.0000.059
methylRawDB-class0.0730.0040.072
methylRawList-class0.0090.0000.009
methylRawListDB-class0.1110.0080.119
normalizeCoverage-methods0.1280.0080.136
percMethylation-methods0.0210.0000.021
pool-methods0.0130.0000.013
processBismarkAln-methods0.0450.0040.050
readMethylDB-methods000
reconstruct-methods0.0170.0000.018
regionCounts0.3240.0000.325
removeComp-methods0.0270.0000.026
reorganize-methods0.1530.0110.114
select-methods0.1330.0120.130
selectByOverlap-methods3.330.143.45
show-methods0.0250.0000.025
tileMethylCounts-methods0.4610.0000.439
unite-methods0.1440.0000.086