Matthias Zytnicki
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/srnadiff |
| Branch: master |
| Last Commit: adb645d |
| Last Changed Date: 2019-01-04 13:51:27 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
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 |
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### Running command:
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### /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
###
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* 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
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL srnadiff
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* 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 | |