Package: srnadiff

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-10-16 05:14:24 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:20:09 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 345.8 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_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/srnadiff.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 10.455   1.17  10.866
runAll      5.868   0.68   5.616
* 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.

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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::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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 78.325   7.850  76.134 

name	user	system	elapsed
plotRegion	10.455	1.170	10.866
readAnnotation	0.368	0.000	0.368
readMiRBaseMatureAnnotation	0.100	0.000	0.111
readMiRBasePreAnnotation	0.057	0.000	0.057
readWholeGenomeAnnotation	0.317	0.000	0.317
regions-method	0.818	0.008	0.826
runAll	5.868	0.680	5.616
sRNADiffExample	0.620	0.008	0.628
sRNADiffExp	0.505	0.008	0.513
setEmissionProbabilities-method	0.549	0.012	0.561
setEmissionThreshold-method	0.542	0.012	0.554
setMergeDistance-method	0.592	0.000	0.592
setMinDepth-method	0.644	0.012	0.656
setMinDifferences-method	0.506	0.004	0.510
setMinOverlap-method	0.537	0.004	0.542
setNThreads-method	0.843	0.004	0.847
setSizes-method	0.787	0.000	0.787
setStrategies-method	0.727	0.008	0.739
setTransitionProbabilities-method	0.536	0.000	0.536
show-sRNADiff-method	0.706	0.000	0.707