| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 633/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epigraHMM 1.9.1 (landing page) Pedro Baldoni
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: epigraHMM |
| Version: 1.9.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings epigraHMM_1.9.1.tar.gz |
| StartedAt: 2023-06-05 21:52:04 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 22:19:04 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 1620.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: epigraHMM.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings epigraHMM_1.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/epigraHMM.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘epigraHMM/DESCRIPTION’ ... OK
* this is package ‘epigraHMM’ version ‘1.9.1’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 29.1Mb
sub-directories of 1Mb or more:
libs 28.8Mb
* 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 ... OK
* 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 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/R/R-4.3.0/site-library/epigraHMM/libs/epigraHMM.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘sprintf’, possibly from ‘sprintf’ (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
epigraHMMDataSetFromBam 16.527 1.306 394.214
segmentGenome 13.700 1.154 21.906
callPatterns 13.760 0.223 13.971
plotPatterns 13.242 0.303 13.516
* 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 ...
‘epigraHMM.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/epigraHMM.Rcheck/00check.log’
for details.
epigraHMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL epigraHMM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘epigraHMM’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c aggregate.cpp -o aggregate.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c computeBIC.cpp -o computeBIC.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c computeQFunction.cpp -o computeQFunction.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c computeViterbiSequence.cpp -o computeViterbiSequence.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c expStep.cpp -o expStep.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c getMarginalProbability.cpp -o getMarginalProbability.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c innerMaxStepProb.cpp -o innerMaxStepProb.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c maxStepProb.cpp -o maxStepProb.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c rbinomVectorized.cpp -o rbinomVectorized.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c reweight.cpp -o reweight.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include -fopenmp -DARMA_USE_HDF5 -fPIC -g -O2 -c simulateMarkovChain.cpp -o simulateMarkovChain.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/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/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -fopenmp -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(epigraHMM)
>
> test_check("epigraHMM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
>
> proc.time()
user system elapsed
84.955 3.458 166.172
epigraHMM.Rcheck/epigraHMM-Ex.timings
| name | user | system | elapsed | |
| addOffsets | 0.383 | 0.004 | 0.387 | |
| callPatterns | 13.760 | 0.223 | 13.971 | |
| callPeaks | 1.080 | 0.016 | 1.052 | |
| cleanCounts | 1.802 | 0.036 | 1.815 | |
| controlEM | 0 | 0 | 0 | |
| epigraHMM | 0.858 | 0.012 | 0.825 | |
| epigraHMMDataSetFromBam | 16.527 | 1.306 | 394.214 | |
| epigraHMMDataSetFromMatrix | 0.136 | 0.000 | 0.136 | |
| estimateTransitionProb | 0.003 | 0.000 | 0.002 | |
| expStep | 0.884 | 0.034 | 0.868 | |
| helas3 | 0.012 | 0.000 | 0.012 | |
| info | 0.910 | 0.050 | 0.909 | |
| initializer | 0.648 | 0.002 | 0.622 | |
| maxStepProb | 0.875 | 0.044 | 0.869 | |
| normalizeCounts | 0.333 | 0.000 | 0.321 | |
| plotCounts | 0.363 | 0.012 | 0.376 | |
| plotPatterns | 13.242 | 0.303 | 13.516 | |
| segmentGenome | 13.700 | 1.154 | 21.906 | |
| simulateMarkovChain | 0 | 0 | 0 | |