Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 642/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigraHMM 1.13.0  (landing page)
Pedro Baldoni
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/epigraHMM
git_branch: devel
git_last_commit: 52c707d
git_last_commit_date: 2024-04-30 11:34:53 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for epigraHMM on palomino4

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.

raw results


Summary

Package: epigraHMM
Version: 1.13.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigraHMM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings epigraHMM_1.13.0.tar.gz
StartedAt: 2024-06-10 02:23:21 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 02:33:15 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 594.9 seconds
RetCode: 0
Status:   OK  
CheckDir: epigraHMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigraHMM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings epigraHMM_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/epigraHMM.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '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 whether package 'epigraHMM' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... 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-3.20-bioc/R/library/epigraHMM/libs/x64/epigraHMM.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
segmentGenome            9.36   1.39   13.52
callPatterns            10.08   0.44   15.61
epigraHMMDataSetFromBam  9.89   0.56   15.06
plotPatterns             8.23   0.75   12.39
* 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/epigraHMM.Rcheck/00check.log'
for details.


Installation output

epigraHMM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL epigraHMM
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'epigraHMM' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/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-3.20-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-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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-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)

Tests output

epigraHMM.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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(epigraHMM)
> 
> test_check("epigraHMM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
  70.12   10.53  117.15 

Example timings

epigraHMM.Rcheck/epigraHMM-Ex.timings

nameusersystemelapsed
addOffsets1.060.001.07
callPatterns10.08 0.4415.61
callPeaks0.900.202.62
cleanCounts0.710.141.35
controlEM000
epigraHMM0.830.112.81
epigraHMMDataSetFromBam 9.89 0.5615.06
epigraHMMDataSetFromMatrix0.090.030.13
estimateTransitionProb000
expStep0.810.132.84
helas30.020.000.02
info0.920.222.54
initializer0.590.071.39
maxStepProb0.850.113.14
normalizeCounts0.150.020.18
plotCounts0.300.010.31
plotPatterns 8.23 0.7512.39
segmentGenome 9.36 1.3913.52
simulateMarkovChain000