Altuna Akalin
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/methylKit |
| git_branch: RELEASE_3_17 |
| git_last_commit: a15614f |
| git_last_commit_date: 2023-04-25 10:48:14 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:20 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 1200/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylKit 1.26.0 (landing page) Altuna Akalin
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the methylKit package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: methylKit |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2023-10-16 03:57:59 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 04:05:05 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 426.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methylKit.Rcheck |
| Warnings: 1 |
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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_1.26.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/methylKit.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 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 '1.26.0'
* 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 C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 12.1Mb
sub-directories of 1Mb or more:
R 1.4Mb
libs 9.4Mb
* 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 ... NOTE
Problems with news in 'NEWS':
Cannot process chunk/lines:
is used with destrand=TRUE argument. It returned less number of CpGs then it was
Cannot process chunk/lines:
supposed to, although returned CpGs had correct methylation and coverage values.
* 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 5.79 0.16 5.94
* 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, 6 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc/meat/methylKit.Rcheck/00check.log'
for details.
methylKit.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL methylKit
###
##############################################################################
##############################################################################
* 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:/rtools43/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:/rtools43/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 -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/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)
methylKit.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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 object is masked from 'package:utils':
findMatches
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
73.34 3.43 84.43
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.02 | 0.00 | 0.01 | |
| adjustMethylC | 0.06 | 0.00 | 0.08 | |
| assocComp-methods | 0.00 | 0.03 | 0.03 | |
| bedgraph-methods | 0.03 | 0.00 | 0.06 | |
| calculateDiffMeth-methods | 5.79 | 0.16 | 5.94 | |
| calculateDiffMethDSS-methods | 0.34 | 0.01 | 0.36 | |
| clusterSamples-methods | 0.03 | 0.02 | 0.05 | |
| dataSim-methods | 0.02 | 0.00 | 0.01 | |
| diffMethPerChr-methods | 0.01 | 0.01 | 0.03 | |
| extract-methods | 0.03 | 0.00 | 0.03 | |
| filterByCoverage-methods | 0.07 | 0.02 | 0.11 | |
| getAssembly-methods | 0.00 | 0.02 | 0.02 | |
| getContext-methods | 0.01 | 0.00 | 0.01 | |
| getCorrelation-methods | 0.08 | 0.00 | 0.13 | |
| getCoverageStats-methods | 0.02 | 0.00 | 0.02 | |
| getDBPath-methods | 0.06 | 0.00 | 0.10 | |
| getData-methods | 0.01 | 0.00 | 0.02 | |
| getMethylDiff-methods | 0.02 | 0.00 | 0.02 | |
| getMethylationStats-methods | 0.01 | 0.01 | 0.03 | |
| getSampleID-methods | 0 | 0 | 0 | |
| getTreatment-methods | 0.00 | 0.01 | 0.02 | |
| makeMethylDB-methods | 0 | 0 | 0 | |
| methRead-methods | 0.33 | 0.07 | 0.62 | |
| methSeg | 0 | 0 | 0 | |
| methylBase-class | 0.02 | 0.00 | 0.02 | |
| methylBaseDB-class | 0.09 | 0.03 | 0.16 | |
| methylDiff-class | 0.03 | 0.00 | 0.03 | |
| methylDiffDB-class | 1.72 | 0.03 | 1.78 | |
| methylRaw-class | 0.06 | 0.01 | 0.08 | |
| methylRawDB-class | 0.11 | 0.00 | 0.14 | |
| methylRawList-class | 0.00 | 0.02 | 0.01 | |
| methylRawListDB-class | 0.21 | 0.06 | 0.41 | |
| normalizeCoverage-methods | 0.33 | 0.02 | 0.45 | |
| percMethylation-methods | 0.01 | 0.00 | 0.02 | |
| pool-methods | 0.00 | 0.01 | 0.01 | |
| processBismarkAln-methods | 0.08 | 0.02 | 0.10 | |
| readMethylDB-methods | 0 | 0 | 0 | |
| reconstruct-methods | 0.01 | 0.00 | 0.01 | |
| regionCounts | 0.30 | 0.00 | 0.29 | |
| removeComp-methods | 0.01 | 0.01 | 0.04 | |
| reorganize-methods | 0.14 | 0.00 | 0.15 | |
| select-methods | 0.10 | 0.07 | 0.19 | |
| selectByOverlap-methods | 2.39 | 0.17 | 3.20 | |
| show-methods | 0.03 | 0.00 | 0.03 | |
| tileMethylCounts-methods | 0.42 | 0.00 | 0.43 | |
| unite-methods | 0.13 | 0.01 | 0.14 | |