Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1208/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylKit 1.31.0 (landing page) Altuna Akalin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
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: 1.31.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylKit_1.31.0.tar.gz |
StartedAt: 2024-07-16 01:38:03 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 01:44:29 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 386.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methylKit.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylKit_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/methylKit.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * 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 '1.31.0' * 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) 13.2.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 13.6Mb sub-directories of 1Mb or more: R 1.4Mb libs 10.8Mb * 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: returns the same object for the same content * checking code 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 ... 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 for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/methylKit.Rcheck/00check.log' for details.
methylKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL methylKit ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'methylKit' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/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_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)': methCall.cpp:908:17: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 908 | for (i = 0; i < len_cigar; i++) | ~~^~~~~~~~~~~ g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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, 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 240 ] > > proc.time() user system elapsed 66.37 3.39 76.25
methylKit.Rcheck/methylKit-Ex.timings
name | user | system | elapsed | |
PCASamples-methods | 0.02 | 0.02 | 0.03 | |
adjustMethylC | 0.08 | 0.00 | 0.08 | |
assocComp-methods | 0.01 | 0.00 | 0.01 | |
bedgraph-methods | 0.05 | 0.00 | 0.05 | |
calculateDiffMeth-methods | 4.45 | 0.11 | 4.56 | |
calculateDiffMethDSS-methods | 0.35 | 0.03 | 0.38 | |
clusterSamples-methods | 0.03 | 0.01 | 0.04 | |
dataSim-methods | 0.02 | 0.00 | 0.02 | |
diffMethPerChr-methods | 0.01 | 0.02 | 0.03 | |
extract-methods | 0.02 | 0.00 | 0.02 | |
filterByCoverage-methods | 0.06 | 0.00 | 0.09 | |
getAssembly-methods | 0.01 | 0.00 | 0.02 | |
getContext-methods | 0.02 | 0.00 | 0.01 | |
getCorrelation-methods | 0.05 | 0.00 | 0.10 | |
getCoverageStats-methods | 0.00 | 0.01 | 0.01 | |
getDBPath-methods | 0.06 | 0.04 | 0.10 | |
getData-methods | 0.02 | 0.00 | 0.01 | |
getMethylDiff-methods | 0.01 | 0.00 | 0.02 | |
getMethylationStats-methods | 0.02 | 0.00 | 0.01 | |
getSampleID-methods | 0.00 | 0.01 | 0.02 | |
getTreatment-methods | 0.01 | 0.00 | 0.01 | |
makeMethylDB-methods | 0 | 0 | 0 | |
methRead-methods | 0.25 | 0.06 | 0.46 | |
methSeg | 0 | 0 | 0 | |
methylBase-class | 0.02 | 0.00 | 0.01 | |
methylBaseDB-class | 0.04 | 0.02 | 0.13 | |
methylDiff-class | 0.02 | 0.00 | 0.01 | |
methylDiffDB-class | 1.47 | 0.02 | 1.49 | |
methylRaw-class | 0.03 | 0.01 | 0.04 | |
methylRawDB-class | 0.09 | 0.28 | 0.39 | |
methylRawList-class | 0 | 0 | 0 | |
methylRawListDB-class | 0.16 | 0.03 | 0.30 | |
normalizeCoverage-methods | 0.16 | 0.00 | 0.28 | |
percMethylation-methods | 0.03 | 0.00 | 0.03 | |
pool-methods | 0.01 | 0.00 | 0.02 | |
processBismarkAln-methods | 0.07 | 0.00 | 0.06 | |
readMethylDB-methods | 0 | 0 | 0 | |
reconstruct-methods | 0.02 | 0.00 | 0.01 | |
regionCounts | 0.23 | 0.00 | 0.24 | |
removeComp-methods | 0.03 | 0.00 | 0.03 | |
reorganize-methods | 0.11 | 0.03 | 0.14 | |
select-methods | 0.08 | 0.04 | 0.14 | |
selectByOverlap-methods | 1.89 | 0.07 | 2.18 | |
show-methods | 0.02 | 0.02 | 0.03 | |
tileMethylCounts-methods | 0.32 | 0.02 | 0.35 | |
unite-methods | 0.10 | 0.01 | 0.17 | |