Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:14 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for epigraHMM on nebbiolo1


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.

raw results

Package 610/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigraHMM 1.4.0  (landing page)
Pedro Baldoni
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/epigraHMM
git_branch: RELEASE_3_15
git_last_commit: 82b8a69
git_last_commit_date: 2022-04-26 12:16:15 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epigraHMM
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings epigraHMM_1.4.0.tar.gz
StartedAt: 2022-10-18 19:37:08 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:43:16 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 367.9 seconds
RetCode: 0
Status:   OK  
CheckDir: epigraHMM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings epigraHMM_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/epigraHMM.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigraHMM/DESCRIPTION’ ... OK
* this is package ‘epigraHMM’ version ‘1.4.0’
* 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
* checking installed package size ... NOTE
  installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
* 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 is not available
File ‘/home/biocbuild/bbs-3.15-bioc/R/library/epigraHMM/libs/epigraHMM.so’:
  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. 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 10.804  0.992  26.317
plotPatterns            10.474  0.493  10.044
segmentGenome            9.196  1.176  13.736
callPatterns             9.987  0.279   9.467
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/epigraHMM.Rcheck/00check.log’
for details.



Installation output

epigraHMM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL epigraHMM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘epigraHMM’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-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-3.15-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -fopenmp -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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)

Tests output

epigraHMM.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 66 ]
> 
> proc.time()
   user  system elapsed 
 59.780   3.335  72.863 

Example timings

epigraHMM.Rcheck/epigraHMM-Ex.timings

nameusersystemelapsed
addOffsets1.3850.0681.453
callPatterns9.9870.2799.467
callPeaks1.1460.0800.827
cleanCounts0.7450.0640.625
controlEM0.0010.0000.000
epigraHMM0.9740.0180.613
epigraHMMDataSetFromBam10.804 0.99226.317
epigraHMMDataSetFromMatrix0.1070.0050.112
estimateTransitionProb0.0030.0000.002
expStep1.0090.0630.695
helas30.0140.0050.012
info1.0320.0140.653
initializer0.7200.0390.498
maxStepProb1.0300.0460.684
normalizeCounts0.2740.0120.219
plotCounts0.3180.0240.341
plotPatterns10.474 0.49310.044
segmentGenome 9.196 1.17613.736
simulateMarkovChain0.0010.0000.001