Kipper Fletez-Brant
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/bnbc |
| Branch: RELEASE_3_10 |
| Last Commit: 4f16142 |
| Last Changed Date: 2019-10-29 13:10:50 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:13:21 -0400 (Wed, 15 Apr 2020).
| Package 190/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bnbc 1.8.0 Kipper Fletez-Brant
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: bnbc |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:bnbc.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings bnbc_1.8.0.tar.gz |
| StartedAt: 2020-04-15 05:13:27 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:19:02 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 334.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bnbc.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:bnbc.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings bnbc_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/bnbc.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bnbc/DESCRIPTION’ ... OK
* this is package ‘bnbc’ version ‘1.8.0’
* 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 ‘bnbc’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
smoothing 28.532 0.016 28.594
bnbc-package 23.900 1.144 25.130
bnbc 19.928 0.136 20.124
ContactGroup-class 8.748 0.312 9.076
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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
‘/home/biocbuild/bbs-3.10-bioc/meat/bnbc.Rcheck/00check.log’
for details.
bnbc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL bnbc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘bnbc’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c update_bands.cpp -o update_bands.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o bnbc.so RcppExports.o update_bands.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-bnbc/00new/bnbc/libs ** R ** data ** 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 (bnbc)
bnbc.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> require("bnbc") || stop("unable to load bnbc")
Loading required package: bnbc
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, which.max, which.min
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
[1] TRUE
> BiocGenerics:::testPackage("bnbc")
RUNIT TEST PROTOCOL -- Wed Apr 15 05:18:59 2020
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
bnbc RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
15.348 0.408 15.846
bnbc.Rcheck/bnbc-Ex.timings
| name | user | system | elapsed | |
| ContactGroup-class | 8.748 | 0.312 | 9.076 | |
| apply_functions | 3.452 | 0.068 | 3.527 | |
| band | 3.384 | 0.052 | 3.436 | |
| bnbc-package | 23.900 | 1.144 | 25.130 | |
| bnbc | 19.928 | 0.136 | 20.124 | |
| getBandIdx | 2.724 | 0.044 | 2.780 | |
| getBandMatrix | 2.664 | 0.056 | 2.722 | |
| groupZeros | 3.076 | 0.044 | 3.126 | |
| smoothing | 28.532 | 0.016 | 28.594 | |