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 11:39 -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 648/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epigraHMM 1.13.0 (landing page) Pedro Baldoni
| 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 | ERROR | skipped | skipped | |||||||||
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 epigraHMM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epigraHMM.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: epigraHMM |
Version: 1.13.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings epigraHMM_1.13.0.tar.gz |
StartedAt: 2024-08-20 22:47:35 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:01:15 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 820.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: epigraHMM.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings epigraHMM_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/epigraHMM.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘epigraHMM/DESCRIPTION’ ... OK * this is package ‘epigraHMM’ 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 ‘epigraHMM’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 22.8Mb sub-directories of 1Mb or more: libs 22.4Mb * 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 ... 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 loading without being on the library search path ... 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 LazyData ... 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 ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/epigraHMM/libs/epigraHMM.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘abort’, possibly from ‘abort’ (C) Found ‘rand_r’, possibly from ‘rand_r’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 segmentGenome 19.319 2.235 30.301 epigraHMMDataSetFromBam 10.799 0.931 27.462 plotPatterns 10.942 0.332 10.758 callPatterns 10.019 0.228 9.700 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/epigraHMM.Rcheck/00check.log’ for details.
epigraHMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL epigraHMM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘epigraHMM’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c aggregate.cpp -o aggregate.o aggregate.cpp: In function ‘arma::mat aggregate(arma::vec, arma::vec)’: aggregate.cpp:26:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26 | while( index >= vec.size() ){ | ~~~~~~^~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c computeBIC.cpp -o computeBIC.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c computeQFunction.cpp -o computeQFunction.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c computeViterbiSequence.cpp -o computeViterbiSequence.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c expStep.cpp -o expStep.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c getMarginalProbability.cpp -o getMarginalProbability.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c innerMaxStepProb.cpp -o innerMaxStepProb.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c maxStepProb.cpp -o maxStepProb.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c rbinomVectorized.cpp -o rbinomVectorized.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c reweight.cpp -o reweight.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fpic -g -O2 -Wall -c simulateMarkovChain.cpp -o simulateMarkovChain.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o epigraHMM.so RcppExports.o aggregate.o computeBIC.o computeQFunction.o computeViterbiSequence.o consensusRejectionControlled.o differentialRejectionControlled.o expStep.o getMarginalProbability.o innerMaxStepProb.o maxStepProb.o rbinomVectorized.o reweight.o simulateMarkovChain.o /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -fopenmp -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-epigraHMM/00new/epigraHMM/libs ** R ** data *** moving datasets to lazyload DB ** 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 ** 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 (epigraHMM)
epigraHMM.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(epigraHMM) > > test_check("epigraHMM") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ] > > proc.time() user system elapsed 67.379 3.368 79.782
epigraHMM.Rcheck/epigraHMM-Ex.timings
name | user | system | elapsed | |
addOffsets | 2.010 | 0.052 | 2.062 | |
callPatterns | 10.019 | 0.228 | 9.700 | |
callPeaks | 1.162 | 0.012 | 0.800 | |
cleanCounts | 0.748 | 0.017 | 0.576 | |
controlEM | 0.001 | 0.000 | 0.000 | |
epigraHMM | 1.013 | 0.036 | 0.647 | |
epigraHMMDataSetFromBam | 10.799 | 0.931 | 27.462 | |
epigraHMMDataSetFromMatrix | 0.106 | 0.000 | 0.107 | |
estimateTransitionProb | 0.002 | 0.000 | 0.002 | |
expStep | 0.922 | 0.023 | 0.581 | |
helas3 | 0.015 | 0.000 | 0.010 | |
info | 0.961 | 0.016 | 0.630 | |
initializer | 0.638 | 0.015 | 0.412 | |
maxStepProb | 0.948 | 0.016 | 0.579 | |
normalizeCounts | 0.284 | 0.004 | 0.221 | |
plotCounts | 0.302 | 0.004 | 0.307 | |
plotPatterns | 10.942 | 0.332 | 10.758 | |
segmentGenome | 19.319 | 2.235 | 30.301 | |
simulateMarkovChain | 0.001 | 0.000 | 0.000 | |