Pedro Baldoni
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/epigraHMM |
| git_branch: RELEASE_3_14 |
| git_last_commit: 67481cd |
| git_last_commit_date: 2022-01-13 17:00:11 -0400 (Thu, 13 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:19 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 591/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epigraHMM 1.2.2 (landing page) Pedro Baldoni
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: epigraHMM |
| Version: 1.2.2 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings epigraHMM_1.2.2.tar.gz |
| StartedAt: 2022-04-12 07:20:02 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 07:25:54 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 352.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epigraHMM.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings epigraHMM_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/epigraHMM.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.2.2’
* 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 30.0Mb
sub-directories of 1Mb or more:
libs 29.6Mb
* 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-3.14-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 10.461 0.663 26.914
callPatterns 9.963 0.403 9.524
segmentGenome 8.711 1.338 13.372
plotPatterns 8.827 0.184 8.219
* 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-3.14-bioc/meat/epigraHMM.Rcheck/00check.log’
for details.
epigraHMM.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL epigraHMM
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘epigraHMM’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -fopenmp -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)
epigraHMM.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
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
60.293 2.713 73.226
epigraHMM.Rcheck/epigraHMM-Ex.timings
| name | user | system | elapsed | |
| addOffsets | 1.408 | 0.092 | 1.500 | |
| callPatterns | 9.963 | 0.403 | 9.524 | |
| callPeaks | 1.409 | 0.082 | 1.072 | |
| cleanCounts | 0.841 | 0.028 | 0.685 | |
| controlEM | 0 | 0 | 0 | |
| epigraHMM | 1.111 | 0.013 | 0.745 | |
| epigraHMMDataSetFromBam | 10.461 | 0.663 | 26.914 | |
| epigraHMMDataSetFromMatrix | 0.142 | 0.016 | 0.158 | |
| estimateTransitionProb | 0.002 | 0.000 | 0.002 | |
| expStep | 1.092 | 0.018 | 0.745 | |
| helas3 | 0.027 | 0.000 | 0.021 | |
| info | 1.157 | 0.025 | 0.781 | |
| initializer | 0.817 | 0.019 | 0.572 | |
| maxStepProb | 1.156 | 0.014 | 0.789 | |
| normalizeCounts | 1.337 | 0.161 | 1.428 | |
| plotCounts | 0.253 | 0.000 | 0.254 | |
| plotPatterns | 8.827 | 0.184 | 8.219 | |
| segmentGenome | 8.711 | 1.338 | 13.372 | |
| simulateMarkovChain | 0 | 0 | 0 | |