| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:27 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 594/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epigraHMM 1.3.2 (landing page) Pedro Baldoni
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: epigraHMM |
| Version: 1.3.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigraHMM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings epigraHMM_1.3.2.tar.gz |
| StartedAt: 2022-03-17 19:01:59 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:08:05 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 366.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epigraHMM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigraHMM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings epigraHMM_1.3.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/epigraHMM.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'epigraHMM/DESCRIPTION' ... OK
* this is package 'epigraHMM' version '1.3.2'
* 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 whether package 'epigraHMM' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
libs 4.7Mb
* 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 'D:/biocbuild/bbs-3.15-bioc/R/library/epigraHMM/libs/x64/epigraHMM.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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
segmentGenome 8.08 2.19 13.68
epigraHMMDataSetFromBam 8.22 0.72 17.93
plotPatterns 8.19 0.33 9.86
callPatterns 8.20 0.25 9.97
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/epigraHMM.Rcheck/00check.log'
for details.
epigraHMM.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL epigraHMM
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'epigraHMM' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
while( index >= vec.size() ){
~~~~~~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c computeBIC.cpp -o computeBIC.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c computeQFunction.cpp -o computeQFunction.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c computeViterbiSequence.cpp -o computeViterbiSequence.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c expStep.cpp -o expStep.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c getMarginalProbability.cpp -o getMarginalProbability.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c innerMaxStepProb.cpp -o innerMaxStepProb.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c maxStepProb.cpp -o maxStepProb.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rbinomVectorized.cpp -o rbinomVectorized.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c reweight.cpp -o reweight.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -fopenmp -DARMA_USE_HDF5 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c simulateMarkovChain.cpp -o simulateMarkovChain.o
C:/rtools40/mingw64/bin/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 -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-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
converting help for package 'epigraHMM'
finding HTML links ... done
addOffsets html
callPatterns html
callPeaks html
cleanCounts html
controlEM html
epigraHMM html
epigraHMMDataSetFromBam html
epigraHMMDataSetFromMatrix html
estimateTransitionProb html
expStep html
helas3 html
info html
initializer html
maxStepProb html
normalizeCounts html
plotCounts html
plotPatterns html
segmentGenome html
simulateMarkovChain html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'consensusDE' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'transcriptR' is missing or broken
done
epigraHMM.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 66 ]
>
> proc.time()
user system elapsed
53.68 4.64 75.45
epigraHMM.Rcheck/epigraHMM-Ex.timings
| name | user | system | elapsed | |
| addOffsets | 0.30 | 0.06 | 0.36 | |
| callPatterns | 8.20 | 0.25 | 9.97 | |
| callPeaks | 0.89 | 0.06 | 2.17 | |
| cleanCounts | 0.74 | 0.02 | 1.14 | |
| controlEM | 0 | 0 | 0 | |
| epigraHMM | 0.86 | 0.06 | 2.23 | |
| epigraHMMDataSetFromBam | 8.22 | 0.72 | 17.93 | |
| epigraHMMDataSetFromMatrix | 0.14 | 0.01 | 0.15 | |
| estimateTransitionProb | 0 | 0 | 0 | |
| expStep | 1.04 | 0.02 | 2.28 | |
| helas3 | 0 | 0 | 0 | |
| info | 0.89 | 0.06 | 2.03 | |
| initializer | 0.46 | 0.05 | 1.57 | |
| maxStepProb | 0.92 | 0.08 | 1.78 | |
| normalizeCounts | 1.11 | 0.04 | 1.34 | |
| plotCounts | 0.23 | 0.00 | 0.24 | |
| plotPatterns | 8.19 | 0.33 | 9.86 | |
| segmentGenome | 8.08 | 2.19 | 13.68 | |
| simulateMarkovChain | 0 | 0 | 0 | |