Pedro Baldoni
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/epigraHMM |
| git_branch: RELEASE_3_16 |
| git_last_commit: 5055b06 |
| git_last_commit_date: 2023-03-22 18:07:04 -0400 (Wed, 22 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:32 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the epigraHMM package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 620/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epigraHMM 1.6.4 (landing page) Pedro Baldoni
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: epigraHMM |
| Version: 1.6.4 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigraHMM.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings epigraHMM_1.6.4.tar.gz |
| StartedAt: 2023-04-11 01:15:03 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:22:24 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 441.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epigraHMM.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigraHMM.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings epigraHMM_1.6.4.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/epigraHMM.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'epigraHMM/DESCRIPTION' ... OK
* this is package 'epigraHMM' version '1.6.4'
* 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 'epigraHMM' can be installed ... OK
* 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 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 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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/epigraHMM/libs/x64/epigraHMM.dll':
Found '_assert', possibly from 'assert' (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. 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 11.31 0.36 15.92
callPatterns 11.06 0.47 14.56
segmentGenome 10.23 0.51 13.78
plotPatterns 9.30 0.68 11.74
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/epigraHMM.Rcheck/00check.log'
for details.
epigraHMM.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL epigraHMM
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'epigraHMM' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare]
26 | while( index >= vec.size() ){
| ~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeBIC.cpp -o computeBIC.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeQFunction.cpp -o computeQFunction.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeViterbiSequence.cpp -o computeViterbiSequence.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c expStep.cpp -o expStep.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getMarginalProbability.cpp -o getMarginalProbability.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c innerMaxStepProb.cpp -o innerMaxStepProb.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c maxStepProb.cpp -o maxStepProb.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rbinomVectorized.cpp -o rbinomVectorized.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c reweight.cpp -o reweight.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulateMarkovChain.cpp -o simulateMarkovChain.o
g++ -shared -s -static-libgcc -o epigraHMM.dll tmp.def 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 -LF:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -fopenmp -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-epigraHMM/00new/epigraHMM/libs/x64
** 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
** 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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
70.15 4.53 100.84
epigraHMM.Rcheck/epigraHMM-Ex.timings
| name | user | system | elapsed | |
| addOffsets | 0.43 | 0.00 | 0.42 | |
| callPatterns | 11.06 | 0.47 | 14.56 | |
| callPeaks | 1.17 | 0.06 | 2.67 | |
| cleanCounts | 0.86 | 0.10 | 1.44 | |
| controlEM | 0 | 0 | 0 | |
| epigraHMM | 1.03 | 0.08 | 2.67 | |
| epigraHMMDataSetFromBam | 11.31 | 0.36 | 15.92 | |
| epigraHMMDataSetFromMatrix | 0.14 | 0.02 | 0.15 | |
| estimateTransitionProb | 0 | 0 | 0 | |
| expStep | 1.12 | 0.14 | 2.22 | |
| helas3 | 0.02 | 0.00 | 0.05 | |
| info | 1.02 | 0.14 | 2.01 | |
| initializer | 0.73 | 0.04 | 1.52 | |
| maxStepProb | 1.0 | 0.1 | 2.2 | |
| normalizeCounts | 1.27 | 0.00 | 1.28 | |
| plotCounts | 0.34 | 0.01 | 0.42 | |
| plotPatterns | 9.30 | 0.68 | 11.74 | |
| segmentGenome | 10.23 | 0.51 | 13.78 | |
| simulateMarkovChain | 0 | 0 | 0 | |