Rory Stark
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/DiffBind |
| Branch: RELEASE_3_6 |
| Last Commit: f010df1 |
| Last Changed Date: 2018-01-19 12:32:21 -0400 (Fri, 19 Jan 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:09:54 -0400 (Thu, 12 Apr 2018).
| Package 363/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DiffBind 2.6.6 Rory Stark
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DiffBind |
| Version: 2.6.6 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DiffBind_2.6.6.tar.gz |
| StartedAt: 2018-04-11 22:56:00 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:05:04 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 544.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DiffBind.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DiffBind_2.6.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DiffBind.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DiffBind/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffBind’ version ‘2.6.6’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘XLConnect’
* 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 ‘DiffBind’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
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 ... NOTE
pv.DBAplotVolcano: no visible binding for global variable ‘Fold’
pv.DBAplotVolcano: no visible binding for global variable ‘Legend’
Undefined global functions or variables:
Fold Legend
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.6-bioc/meat/DiffBind.Rcheck/00check.log’
for details.
DiffBind.Rcheck/00install.out
* installing *source* package ‘DiffBind’ ... ** libs g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c bamReader.cpp -o bamReader.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c bedReader.cpp -o bedReader.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c bitBucket.cpp -o bitBucket.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c croi_func.cpp -o croi_func.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c croi_main.cpp -o croi_main.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c densitySet.cpp -o densitySet.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c iBucket.cpp -o iBucket.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c interval.cpp -o interval.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c intervalDensity.cpp -o intervalDensity.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c intervalNode.cpp -o intervalNode.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c intervalSet.cpp -o intervalSet.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c intervalTree.cpp -o intervalTree.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c merge.cpp -o merge.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c mergeOne.c -o mergeOne.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c nodeGroup.cpp -o nodeGroup.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c peakOrder.cpp -o peakOrder.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c reader.cpp -o reader.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c sequence.cpp -o sequence.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o DiffBind.so RcppExports.o bamReader.o bedReader.o bitBucket.o croi_func.o croi_main.o densitySet.o iBucket.o interval.o intervalDensity.o intervalNode.o intervalSet.o intervalTree.o merge.o mergeOne.o nodeGroup.o peakOrder.o reader.o sequence.o util.o /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/DiffBind.Rcheck/DiffBind/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (DiffBind)
DiffBind.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(DiffBind)
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
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
Loading required package: SummarizedExperiment
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
>
> test_check("DiffBind")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 66 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
24.240 0.248 26.143
DiffBind.Rcheck/DiffBind-Ex.timings
| name | user | system | elapsed |