Rory Stark
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 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) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 554/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DiffBind 3.15.0 (landing page) Rory Stark
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: DiffBind |
| Version: 3.15.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DiffBind.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DiffBind_3.15.0.tar.gz |
| StartedAt: 2024-06-10 01:59:13 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 02:12:15 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 781.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DiffBind.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DiffBind.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DiffBind_3.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/DiffBind.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 whether package 'DiffBind' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
installed size is 15.0Mb
sub-directories of 1Mb or more:
data 2.0Mb
extra 1.3Mb
libs 10.8Mb
* 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 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/DiffBind/libs/x64/DiffBind.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dba.contrast 40.72 0.67 41.41
dba.plotVenn 29.49 0.47 30.04
dba.normalize 25.29 0.36 25.65
dba.plotMA 14.87 0.31 15.20
dba.analyze 14.31 0.36 14.67
dba.blacklist 9.22 0.09 9.32
dba.plotHeatmap 8.16 0.14 8.30
dba.report 5.69 0.12 5.81
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/DiffBind.Rcheck/00check.log'
for details.
DiffBind.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DiffBind ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'DiffBind' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bamReader.cpp -o bamReader.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bedReader.cpp -o bedReader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bitBucket.cpp -o bitBucket.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c croi_func.cpp -o croi_func.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c croi_main.cpp -o croi_main.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densitySet.cpp -o densitySet.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c iBucket.cpp -o iBucket.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interval.cpp -o interval.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c intervalDensity.cpp -o intervalDensity.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c intervalNode.cpp -o intervalNode.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c intervalSet.cpp -o intervalSet.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c intervalTree.cpp -o intervalTree.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c merge.cpp -o merge.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mergeOne.c -o mergeOne.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nodeGroup.cpp -o nodeGroup.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c peakOrder.cpp -o peakOrder.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c reader.cpp -o reader.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequence.cpp -o sequence.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o g++ -std=gnu++17 -shared -s -static-libgcc -o DiffBind.dll tmp.def 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 F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-DiffBind/00new/DiffBind/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DiffBind)
DiffBind.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
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> 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 1 | PASS 117 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_normalize.R:1:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 117 ]
>
> proc.time()
user system elapsed
32.53 5.15 41.29
DiffBind.Rcheck/DiffBind-Ex.timings
| name | user | system | elapsed | |
| dba | 1.38 | 0.08 | 1.47 | |
| dba.analyze | 14.31 | 0.36 | 14.67 | |
| dba.blacklist | 9.22 | 0.09 | 9.32 | |
| dba.contrast | 40.72 | 0.67 | 41.41 | |
| dba.count | 1.80 | 0.13 | 2.03 | |
| dba.load | 0.08 | 0.01 | 0.11 | |
| dba.mask | 0.04 | 0.05 | 0.09 | |
| dba.normalize | 25.29 | 0.36 | 25.65 | |
| dba.overlap | 0.45 | 0.06 | 0.51 | |
| dba.peakset | 1.76 | 0.10 | 2.08 | |
| dba.plotBox | 0.36 | 0.03 | 0.39 | |
| dba.plotHeatmap | 8.16 | 0.14 | 8.30 | |
| dba.plotMA | 14.87 | 0.31 | 15.20 | |
| dba.plotPCA | 1.02 | 0.06 | 1.08 | |
| dba.plotProfile | 0.14 | 0.05 | 0.19 | |
| dba.plotVenn | 29.49 | 0.47 | 30.04 | |
| dba.plotVolcano | 3.29 | 0.11 | 3.41 | |
| dba.report | 5.69 | 0.12 | 5.81 | |
| dba.save | 0 | 0 | 0 | |
| dba.show | 0.37 | 0.03 | 0.41 | |
| print.DBA | 0.07 | 0.04 | 0.09 | |
| tamoxifen | 0.62 | 0.04 | 0.67 | |