Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:49:45 -0400 (Tue, 09 Apr 2019).
Package 1552/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
srnadiff 1.3.1 Matthias Zytnicki
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: srnadiff |
Version: 1.3.1 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings srnadiff_1.3.1.tar.gz |
StartedAt: 2019-04-09 03:51:36 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 03:57:06 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 329.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: srnadiff.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings srnadiff_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/srnadiff.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘srnadiff/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘srnadiff’ version ‘1.3.1’ * 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 ‘srnadiff’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: extdata 1.8Mb libs 3.4Mb * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed plotRegion 6.552 1.039 6.174 runAll 5.366 0.682 5.184 * 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/srnadiff.Rcheck/00check.log’ for details.
srnadiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL srnadiff ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘srnadiff’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_hmm.cpp -o rcpp_hmm.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_naive.cpp -o rcpp_naive.o rcpp_naive.cpp: In function ‘Rcpp::DataFrame rcpp_naive(Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<13> > >&, Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<13> > >&, Rcpp::IntegerVector&, int, int, int)’: rcpp_naive.cpp:80:27: warning: ‘start’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (addElement(start, iterator.getPosition(), chromosome, starts, ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ends, chromosomes, first, distance, size)) { ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_slice.cpp -o rcpp_slice.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_utils.cpp -o rcpp_utils.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c srnadiff_init.c -o srnadiff_init.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o srnadiff.so RcppExports.o rcpp_hmm.o rcpp_naive.o rcpp_slice.o rcpp_utils.o srnadiff_init.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-srnadiff/00new/srnadiff/libs ** R ** inst ** 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 (srnadiff)
srnadiff.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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(srnadiff) > > test_check("srnadiff") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 28 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 71.263 6.892 67.994
srnadiff.Rcheck/srnadiff-Ex.timings
name | user | system | elapsed | |
plotRegion | 6.552 | 1.039 | 6.174 | |
readAnnotation | 0.252 | 0.000 | 0.252 | |
readMiRBaseMatureAnnotation | 0.082 | 0.000 | 0.099 | |
readMiRBasePreAnnotation | 0.046 | 0.000 | 0.046 | |
readWholeGenomeAnnotation | 0.211 | 0.003 | 0.214 | |
regions-method | 0.706 | 0.000 | 0.830 | |
runAll | 5.366 | 0.682 | 5.184 | |
sRNADiffExample | 0.789 | 0.008 | 0.797 | |
sRNADiffExp | 0.631 | 0.004 | 0.635 | |
setEmissionProbabilities-method | 0.765 | 0.004 | 0.769 | |
setEmissionThreshold-method | 0.630 | 0.004 | 0.634 | |
setMergeDistance-method | 0.623 | 0.020 | 0.643 | |
setMinDepth-method | 0.707 | 0.000 | 0.707 | |
setMinDifferences-method | 0.576 | 0.004 | 0.580 | |
setMinOverlap-method | 0.545 | 0.000 | 0.545 | |
setNThreads-method | 0.795 | 0.012 | 0.807 | |
setSizes-method | 0.785 | 0.008 | 0.793 | |
setStrategies-method | 0.711 | 0.004 | 0.715 | |
setTransitionProbabilities-method | 0.631 | 0.004 | 0.635 | |
show-sRNADiff-method | 0.552 | 0.004 | 0.557 | |