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This page was generated on 2024-06-21 13:21 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 555/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffBind 3.15.0  (landing page)
Rory Stark
Snapshot Date: 2024-06-20 14:00 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/DiffBind
git_branch: devel
git_last_commit: 09998c6
git_last_commit_date: 2024-04-30 10:25:38 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for DiffBind on nebbiolo2

To the developers/maintainers of the DiffBind package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DiffBind.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DiffBind
Version: 3.15.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DiffBind_3.15.0.tar.gz
StartedAt: 2024-06-20 22:34:40 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 22:46:28 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 707.2 seconds
RetCode: 0
Status:   OK  
CheckDir: DiffBind.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DiffBind_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DiffBind.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DiffBind/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffBind’ version ‘3.15.0’
* 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 ‘DiffBind’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data    2.0Mb
    extra   1.3Mb
    libs    6.0Mb
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) NEWS.Rd:106-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:431-438: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:440-446: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:450-456: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:96-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:102-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:126-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:128-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:102-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:104-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:116-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:118-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:120-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:122-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:96-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:55-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:62-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:92-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:217-219: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:221: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:223-226: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:233-234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:236-237: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:253: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:257-258: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:267-268: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:270-271: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotHeatmap.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotHeatmap.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotHeatmap.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:53-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:58-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:64-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:81-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:89-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:102-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:116-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:123-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:130-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:136-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:142-145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:148-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:153-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:158-159: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:162-163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:166-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:170-171: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:174-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:178-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:183-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:188-190: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:193-195: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:198-200: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:203-204: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:207-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:211-212: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:215-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:219-220: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:223-224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:227-228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:231-232: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:235-236: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/DiffBind/libs/DiffBind.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
dba.contrast    34.566  0.752  35.318
dba.plotVenn    22.503  0.524  23.078
dba.normalize   18.469  0.192  18.689
dba.plotMA      13.412  0.696  14.109
dba.analyze     11.583  0.932  12.515
dba.plotHeatmap  6.673  0.432   6.975
dba.blacklist    6.408  0.188   6.631
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DiffBind.Rcheck/00check.log’
for details.


Installation output

DiffBind.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DiffBind
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘DiffBind’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c bamReader.cpp -o bamReader.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c bedReader.cpp -o bedReader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c bitBucket.cpp -o bitBucket.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c croi_func.cpp -o croi_func.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c croi_main.cpp -o croi_main.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c densitySet.cpp -o densitySet.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c iBucket.cpp -o iBucket.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c interval.cpp -o interval.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c intervalDensity.cpp -o intervalDensity.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c intervalNode.cpp -o intervalNode.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c intervalSet.cpp -o intervalSet.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c intervalTree.cpp -o intervalTree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c merge.cpp -o merge.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c mergeOne.c -o mergeOne.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c nodeGroup.cpp -o nodeGroup.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c peakOrder.cpp -o peakOrder.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c reader.cpp -o reader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c sequence.cpp -o sequence.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c util.cpp -o util.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o DiffBind.so RcppExports.o bamReader.o bam_plbuf.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-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-DiffBind/00new/DiffBind/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 (DiffBind)

Tests output

DiffBind.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

Attaching package: 'BiocGenerics'

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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

 >>> DiffBind 3.15.0
> 
> test_check("DiffBind")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 141 ]
> 
> proc.time()
   user  system elapsed 
 86.245   1.774  88.039 

Example timings

DiffBind.Rcheck/DiffBind-Ex.timings

nameusersystemelapsed
dba2.5490.3382.932
dba.analyze11.583 0.93212.515
dba.blacklist6.4080.1886.631
dba.contrast34.566 0.75235.318
dba.count1.7980.0401.860
dba.load0.0730.0000.073
dba.mask0.0560.0000.072
dba.normalize18.469 0.19218.689
dba.overlap0.4960.0080.526
dba.peakset1.2450.1171.378
dba.plotBox0.3990.0160.415
dba.plotHeatmap6.6730.4326.975
dba.plotMA13.412 0.69614.109
dba.plotPCA1.3490.0441.393
dba.plotProfile0.1940.0120.205
dba.plotVenn22.503 0.52423.078
dba.plotVolcano2.6010.0282.629
dba.report3.6060.0363.641
dba.save000
dba.show0.4240.0280.452
print.DBA0.0760.0040.080
tamoxifen0.4720.0080.480