Matthias Zytnicki
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/srnadiff |
| Branch: RELEASE_3_8 |
| Last Commit: 1c2d7d9 |
| Last Changed Date: 2019-01-04 13:51:31 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:05:12 -0400 (Tue, 16 Apr 2019).
| Package 1504/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| srnadiff 1.2.1 Matthias Zytnicki
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: srnadiff |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings srnadiff_1.2.1.tar.gz |
| StartedAt: 2019-04-16 02:58:02 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:04:14 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 372.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: srnadiff.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings srnadiff_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/srnadiff.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.1’
* 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 ... 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 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 8.521 1.451 8.604
runAll 5.979 1.170 5.755
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/srnadiff.Rcheck/00check.log’
for details.
srnadiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL srnadiff ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘srnadiff’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_hmm.cpp -o rcpp_hmm.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_naive.cpp -o rcpp_naive.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_slice.cpp -o rcpp_slice.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_utils.cpp -o rcpp_utils.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c srnadiff_init.c -o srnadiff_init.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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 * DONE (srnadiff)
srnadiff.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
78.543 12.690 76.609
srnadiff.Rcheck/srnadiff-Ex.timings
| name | user | system | elapsed | |
| plotRegion | 8.521 | 1.451 | 8.604 | |
| readAnnotation | 0.340 | 0.004 | 0.347 | |
| readMiRBaseMatureAnnotation | 0.113 | 0.002 | 0.117 | |
| readMiRBasePreAnnotation | 0.069 | 0.001 | 0.070 | |
| readWholeGenomeAnnotation | 0.289 | 0.003 | 0.350 | |
| regions-method | 0.896 | 0.021 | 0.924 | |
| runAll | 5.979 | 1.170 | 5.755 | |
| sRNADiffExample | 0.822 | 0.044 | 0.882 | |
| sRNADiffExp | 0.752 | 0.024 | 0.784 | |
| setEmissionProbabilities-method | 0.714 | 0.015 | 0.738 | |
| setEmissionThreshold-method | 0.685 | 0.017 | 0.709 | |
| setMergeDistance-method | 0.715 | 0.015 | 0.740 | |
| setMinDepth-method | 0.739 | 0.017 | 0.765 | |
| setMinDifferences-method | 0.718 | 0.015 | 0.740 | |
| setMinOverlap-method | 0.749 | 0.018 | 0.778 | |
| setNThreads-method | 0.880 | 0.018 | 0.899 | |
| setSizes-method | 0.921 | 0.022 | 0.948 | |
| setStrategies-method | 0.871 | 0.019 | 0.956 | |
| setTransitionProbabilities-method | 0.889 | 0.019 | 0.915 | |
| show-sRNADiff-method | 0.865 | 0.016 | 0.944 | |