Build/check report for BioC 3.17 - CHECK results for methylKit on palomino5

Hostname	OS	Arch (*)	R version	Installed pkgs
palomino5	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"	4165
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*

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylKit.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings methylKit_1.25.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/methylKit.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'methylKit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylKit' version '1.25.0'
* 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 whether package 'methylKit' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   9.2Mb
* 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 ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/methylKit/libs/x64/methylKit.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 4.89    0.2     5.1
* 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 WARNING, 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/methylKit.Rcheck/00check.log'
for details.

Installation output

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###
### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL methylKit
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'methylKit' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 [-Wmaybe-uninitialized]
  687 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:24: note: 'CHGout' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
  686 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:15: note: 'CHHout' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:685:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
  685 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:9: note: 'out' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
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 [-Wmaybe-uninitialized]
 1014 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:24: note: 'CHGout' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:1013:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
 1013 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:15: note: 'CHHout' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:1012:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
 1012 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:9: note: 'out' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
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 [-Wmaybe-uninitialized]
 1244 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1142:24: note: 'CHGout' was declared here
 1142 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:1243:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
 1243 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1142:15: note: 'CHHout' was declared here
 1142 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:1242:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
 1242 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1142:9: note: 'out' was declared here
 1142 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-methylKit/00new/methylKit/libs/x64
** 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
** 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


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 
  61.29    2.89   68.20

Example timings

name	user	system	elapsed
PCASamples-methods	0.01	0.02	0.03
adjustMethylC	0.14	0.00	0.14
assocComp-methods	0.02	0.01	0.03
bedgraph-methods	0.02	0.00	0.03
calculateDiffMeth-methods	4.89	0.20	5.10
calculateDiffMethDSS-methods	0.25	0.07	0.31
clusterSamples-methods	0.06	0.00	0.06
dataSim-methods	0.03	0.00	0.03
diffMethPerChr-methods	0.02	0.00	0.02
extract-methods	0.01	0.01	0.03
filterByCoverage-methods	0.03	0.03	0.08
getAssembly-methods	0.02	0.00	0.01
getContext-methods	0.01	0.00	0.02
getCorrelation-methods	0.07	0.00	0.09
getCoverageStats-methods	0.00	0.03	0.03
getDBPath-methods	0.04	0.00	0.08
getData-methods	0.02	0.00	0.02
getMethylDiff-methods	0.01	0.00	0.01
getMethylationStats-methods	0.02	0.00	0.02
getSampleID-methods	0.02	0.00	0.01
getTreatment-methods	0.01	0.00	0.02
makeMethylDB-methods	0	0	0
methRead-methods	0.31	0.08	0.44
methSeg	0	0	0
methylBase-class	0.02	0.00	0.01
methylBaseDB-class	0.06	0.03	0.10
methylDiff-class	0.05	0.00	0.04
methylDiffDB-class	1.72	0.04	1.77
methylRaw-class	0.08	0.00	0.08
methylRawDB-class	0.09	0.01	0.12
methylRawList-class	0.02	0.00	0.02
methylRawListDB-class	0.15	0.03	0.25
normalizeCoverage-methods	0.10	0.00	0.25
percMethylation-methods	0.01	0.00	0.01
pool-methods	0.00	0.02	0.02
processBismarkAln-methods	0.03	0.04	0.08
readMethylDB-methods	0	0	0
reconstruct-methods	0.01	0.00	0.02
regionCounts	0.24	0.02	0.25
removeComp-methods	0.04	0.00	0.04
reorganize-methods	0.15	0.00	0.15
select-methods	0.09	0.02	0.11
selectByOverlap-methods	1.97	0.09	2.14
show-methods	0.02	0.00	0.01
tileMethylCounts-methods	0.37	0.02	0.41
unite-methods	0.08	0.00	0.11

CHECK results for methylKit on palomino5

Summary

Command output

Installation output

Tests output

Example timings