Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:44 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1280/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mitoClone2 1.13.0 (landing page) Benjamin Story
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 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: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mitoClone2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mitoClone2_1.13.0.tar.gz |
StartedAt: 2024-12-22 21:47:18 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 21:53:51 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 393.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mitoClone2.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mitoClone2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mitoClone2_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mitoClone2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mitoClone2’ version ‘1.13.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘mitoClone2’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * 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 ... NOTE mitoPlot: no visible binding for global variable ‘gene’ Undefined global functions or variables: gene * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'mitoPlot.Rd': mitoPlot Code: function(variants, patient = NULL, genome = "hg38", customGenome = NULL, showLegend = TRUE, showLabel = TRUE) Docs: function(variants, patient = NULL, genome = "hg38", showLegend = TRUE, showLabel = TRUE) Argument names in code not in docs: customGenome Mismatches in argument names: Position: 4 Code: customGenome Docs: showLegend Position: 5 Code: showLegend Docs: showLabel Codoc mismatches from Rd file 'mutationCallsFromCohort.Rd': mutationCallsFromCohort Code: function(BaseCounts, sites, patient, MINREADS = 5, MINCELL = 20, MINFRAC = 0.1, MINCELLS.PATIENT = 10, MINFRAC.PATIENT = 0.01, MINFRAC.OTHER = 0.1, USE.REFERENCE = TRUE, genome = "hg38", customGenome = NULL) Docs: function(BaseCounts, sites, patient, MINREADS = 5, MINCELL = 20, MINFRAC = 0.1, MINCELLS.PATIENT = 10, MINFRAC.PATIENT = 0.01, MINFRAC.OTHER = 0.1, USE.REFERENCE = TRUE, genome = "hg38") Argument names in code not in docs: customGenome Codoc mismatches from Rd file 'mutationCallsFromExclusionlist.Rd': mutationCallsFromExclusionlist Code: function(BaseCounts, lim.cov = 20, min.af = 0.2, min.num.samples = 0.01 * length(BaseCounts), min.af.universal = min.af, universal.var.cells = 0.95 * length(BaseCounts), exclusionlists.use = exclusionlists, max.var.na = 0.5, max.cell.na = 0.95, genome = "hg38", customDNA = NULL, ncores = 1, ...) Docs: function(BaseCounts, lim.cov = 20, min.af = 0.2, min.num.samples = 0.01 * length(BaseCounts), min.af.universal = min.af, universal.var.cells = 0.95 * length(BaseCounts), exclusionlists.use = exclusionlists, max.var.na = 0.5, max.cell.na = 0.95, genome = "hg38", ncores = 1, ...) Argument names in code not in docs: customDNA Mismatches in argument names: Position: 11 Code: customDNA Docs: ncores Position: 12 Code: ncores Docs: ... * 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 ... INFO 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 ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/mitoClone2/libs/mitoClone2.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_sprintf’, possibly from ‘sprintf’ (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 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 70.638 2.096 73.132 * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.Rcheck/00check.log’ for details.
mitoClone2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mitoClone2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘mitoClone2’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite mkdir -p "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" cp scite "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" rm scite clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c bam2R_10x.cpp -o bam2R_10x.o bam2R_10x.cpp:6:2: warning: '/*' within block comment [-Wcomment] /************************************************************************************** ^ bam2R_10x.cpp:8:1: warning: '/*' within block comment [-Wcomment] /********************************************************************** ^ bam2R_10x.cpp:21:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:3:9: note: previous definition is here #define R_NO_REMAP 1 ^ bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable] int bc_absent; ^ bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable] hts_itr_t *iter = NULL; ^ bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ 6 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o mitoClone2.so bam2R_10x.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-mitoClone2/00new/mitoClone2/libs ** 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 ** 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 (mitoClone2)
mitoClone2.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 15.986 0.716 16.789
mitoClone2.Rcheck/mitoClone2-Ex.timings
name | user | system | elapsed | |
bam2R_10x | 1.203 | 0.027 | 1.238 | |
baseCountsFromBamList | 0.138 | 0.004 | 0.144 | |
clusterMetaclones | 0.044 | 0.002 | 0.047 | |
getAlleleCount | 0.007 | 0.001 | 0.008 | |
getCloneLikelihood | 0.005 | 0.001 | 0.006 | |
getVarsCandidate | 0.005 | 0.001 | 0.006 | |
mitoPlot | 0.769 | 0.055 | 0.829 | |
mut2GR | 0.188 | 0.005 | 0.195 | |
mutationCallsFromCohort | 1.014 | 0.047 | 1.067 | |
mutationCallsFromExclusionlist | 2.074 | 0.062 | 2.146 | |
mutationCallsFromMatrix | 1.191 | 0.075 | 1.273 | |
overwriteMetaclones | 0.016 | 0.001 | 0.017 | |
plotClones | 0.288 | 0.013 | 0.303 | |
pullcountsVars | 1.115 | 0.010 | 1.131 | |
quick_cluster | 0.102 | 0.007 | 0.110 | |
removeWindow | 0.398 | 0.003 | 0.402 | |
setVarsCandidate | 0.006 | 0.001 | 0.006 | |
varCluster | 70.638 | 2.096 | 73.132 | |