Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1272/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mitoClone2 1.11.0 (landing page) Benjamin Story
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the mitoClone2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mitoClone2.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: mitoClone2 |
Version: 1.11.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mitoClone2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mitoClone2_1.11.0.tar.gz |
StartedAt: 2024-08-21 02:46:59 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 02:55:05 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 486.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mitoClone2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mitoClone2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mitoClone2_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/mitoClone2.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 'mitoClone2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'mitoClone2' version '1.11.0' * package encoding: UTF-8 * 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 'mitoClone2' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 14.4Mb sub-directories of 1Mb or more: SCITE 3.2Mb libs 10.0Mb * 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 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 ... OK * 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 R/sysdata.rda ... 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-3.20-bioc/R/library/mitoClone2/libs/x64/mitoClone2.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 varCluster 9.83 0.49 66.53 * 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: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/mitoClone2.Rcheck/00check.log' for details.
mitoClone2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL mitoClone2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'mitoClone2' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite ../inst/SCITEpkg/findBestTrees.cpp:58:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch] 58 | double gamma = 1; | ^~~~~ mkdir -p "F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" cp scite "F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" rm scite g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R_10x.cpp -o bam2R_10x.o bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment] 6 | /************************************************************************************** | bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment] 8 | /********************************************************************** | bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)': bam2R_10x.cpp:75:17: warning: unused variable 'bc_absent' [-Wunused-variable] 75 | int bc_absent; | ^~~~~~~~~ bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable] 158 | hts_itr_t *iter = NULL; | ^~~~ bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable] 161 | int c = 0; | ^ g++ -std=gnu++17 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o F:/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 -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-mitoClone2/00new/mitoClone2/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (mitoClone2)
mitoClone2.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(mitoClone2) > > test_check("mitoClone2") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 15.12 0.92 16.07
mitoClone2.Rcheck/mitoClone2-Ex.timings
name | user | system | elapsed | |
bam2R_10x | 0.34 | 0.00 | 0.38 | |
baseCountsFromBamList | 0.14 | 0.00 | 0.14 | |
clusterMetaclones | 0.05 | 0.00 | 0.06 | |
getAlleleCount | 0.00 | 0.00 | 0.02 | |
getCloneLikelihood | 0.01 | 0.00 | 0.02 | |
getVarsCandidate | 0.02 | 0.00 | 0.01 | |
mitoPlot | 1.00 | 0.05 | 1.05 | |
mut2GR | 0.15 | 0.02 | 0.18 | |
mutationCallsFromCohort | 2.11 | 0.06 | 2.17 | |
mutationCallsFromExclusionlist | 2.44 | 0.14 | 2.58 | |
mutationCallsFromMatrix | 1.31 | 0.07 | 1.37 | |
overwriteMetaclones | 0.03 | 0.00 | 0.03 | |
plotClones | 0.30 | 0.01 | 0.32 | |
pullcountsVars | 1.14 | 0.00 | 1.14 | |
quick_cluster | 0.11 | 0.00 | 0.11 | |
removeWindow | 0.42 | 0.00 | 0.42 | |
setVarsCandidate | 0 | 0 | 0 | |
varCluster | 9.83 | 0.49 | 66.53 | |