Tsu-Pei Chiu
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DNAshapeR |
| Branch: RELEASE_3_12 |
| Last Commit: 383b9b2 |
| Last Changed Date: 2020-10-27 11:12:34 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:22 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the DNAshapeR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 501/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DNAshapeR 1.18.0 (landing page) Tsu-Pei Chiu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DNAshapeR |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DNAshapeR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DNAshapeR_1.18.0.tar.gz |
| StartedAt: 2021-05-06 01:04:10 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:07:18 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 187.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNAshapeR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DNAshapeR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DNAshapeR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/DNAshapeR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNAshapeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNAshapeR’ version ‘1.18.0’
* 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 ‘DNAshapeR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.5Mb
sub-directories of 1Mb or more:
extdata 2.6Mb
libs 5.8Mb
* 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 ... NOTE
readNonStandardFastaFile: no visible binding for global variable
‘line_to_append’
Undefined global functions or variables:
line_to_append
* 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 (user + system) or elapsed time > 5s
user system elapsed
heatShape 21.336 0.092 21.462
getShape 20.932 0.172 21.147
plotShape 18.104 0.044 18.186
getFasta 9.288 0.148 9.511
* 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
‘/home/biocbuild/bbs-3.12-bioc/meat/DNAshapeR.Rcheck/00check.log’
for details.
DNAshapeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL DNAshapeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘DNAshapeR’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c OptionParser.cpp -o OptionParser.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c Output.cpp -o Output.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c ReadData.cpp -o ReadData.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c SNP.cpp -o SNP.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c ShapePrediction.cpp -o ShapePrediction.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c TableCompiler.cpp -o TableCompiler.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c map.cpp -o map.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c prediction.cpp -o prediction.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c properties.cpp -o properties.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utilities.cpp -o utilities.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o DNAshapeR.so OptionParser.o Output.o RcppExports.o ReadData.o SNP.o ShapePrediction.o TableCompiler.o map.o prediction.o properties.o utilities.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-DNAshapeR/00new/DNAshapeR/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 (DNAshapeR)
DNAshapeR.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(DNAshapeR)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
> test_check("DNAshapeR")
Read 2 items
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
>
> proc.time()
user system elapsed
5.476 0.164 5.652
DNAshapeR.Rcheck/DNAshapeR-Ex.timings
| name | user | system | elapsed | |
| encodeSeqShape | 0.668 | 0.000 | 0.790 | |
| getFasta | 9.288 | 0.148 | 9.511 | |
| getShape | 20.932 | 0.172 | 21.147 | |
| heatShape | 21.336 | 0.092 | 21.462 | |
| plotShape | 18.104 | 0.044 | 18.186 | |
| readShape | 0.244 | 0.000 | 0.244 | |
| trackShape | 0.664 | 0.000 | 0.673 | |