Rory Stark
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/DiffBind |
| git_branch: RELEASE_3_18 |
| git_last_commit: 00284e8 |
| git_last_commit_date: 2023-10-24 09:48:02 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:37 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 558/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DiffBind 3.12.0 (landing page) Rory Stark
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DiffBind |
| Version: 3.12.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DiffBind_3.12.0.tar.gz |
| StartedAt: 2023-11-02 09:58:36 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 10:08:47 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 610.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DiffBind.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DiffBind_3.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DiffBind.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DiffBind/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffBind’ version ‘3.12.0’
* 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 (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 11.7Mb
sub-directories of 1Mb or more:
data 2.0Mb
extra 1.3Mb
libs 7.4Mb
* 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 loading without being on the library search path ... OK
* checking 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 ... 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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.1/site-library/DiffBind/libs/DiffBind.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘sprintf’, possibly from ‘sprintf’ (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 ... ERROR
Running examples in ‘DiffBind-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dba.contrast
> ### Title: Set up contrasts for differential binding affinity analysis
> ### Aliases: dba.contrast
>
> ### ** Examples
>
> # Set up an explicit contrast
> data(tamoxifen_counts)
> tamoxifen <- dba.contrast(tamoxifen, contrast=c("Condition","Responsive","Resistant"))
Computing results names...
> tamoxifen
11 Samples, 2845 sites in matrix:
ID Tissue Factor Condition Treatment Replicate Reads FRiP
1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16
2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15
3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31
4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19
5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25
6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11
7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06
8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22
9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14
10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33
11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22
Design: [~Condition] | 1 Contrast:
Factor Group Samples Group2 Samples2
1 Condition Responsive 7 Resistant 4
> tamoxifen <- dba.analyze(tamoxifen)
Normalize DESeq2 with defaults...
Analyzing...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
> dba.show(tamoxifen,bContrasts=TRUE)
Factor Group Samples Group2 Samples2 DB.DESeq2
1 Condition Responsive 7 Resistant 4 246
>
> # Add another contrast
> tamoxifen <- dba.contrast(tamoxifen, contrast=c("Tissue","MCF7","BT474"))
Replacing design and removing analysis.
Computing results names...
> dba.show(tamoxifen,bDesign=TRUE)
[1] "~Condition + Tissue"
>
> # Change design
> tamoxifen <- dba.contrast(tamoxifen,design="~Tissue + Condition")
Replacing design.
Computing results names...
> tamoxifen <- dba.analyze(tamoxifen)
Analyzing...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
> tamoxifen
11 Samples, 2845 sites in matrix:
ID Tissue Factor Condition Treatment Replicate Reads FRiP
1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16
2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15
3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31
4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19
5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25
6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11
7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06
8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22
9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14
10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33
11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22
Design: [~Tissue + Condition] | 2 Contrasts:
Factor Group Samples Group2 Samples2 DB.DESeq2
1 Condition Responsive 7 Resistant 4 783
2 Tissue MCF7 5 BT474 2 988
>
> # Automatically add all contrasts between sample groups
> # where at least THREE samples have the same factor value
> data(tamoxifen_counts)
> tamoxifen <- dba.contrast(tamoxifen)
Computing results names...
> tamoxifen
11 Samples, 2845 sites in matrix:
ID Tissue Factor Condition Treatment Replicate Reads FRiP
1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16
2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15
3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31
4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19
5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25
6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11
7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06
8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22
9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14
10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33
11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22
Design: [~Condition] | 1 Contrast:
Factor Group Samples Group2 Samples2
1 Condition Resistant 4 Responsive 7
>
> # Automatically add all contrasts between sample groups
> # where at least TWO samples have the same factor value
> tamoxifen <- dba.contrast(tamoxifen, minMembers=2)
Clearing existing contrasts.
> dba.show(tamoxifen,bContrasts=TRUE)
Factor Group Samples Group2 Samples2
1 Condition Resistant 4 Responsive 7
>
> ### Use of complex contrasts
> data(tamoxifen_counts)
> tamoxifen <- dba.contrast(tamoxifen, contrast=c("Tissue","BT474","MCF7"))
Computing results names...
> dba.contrast(tamoxifen, bGetCoefficients=TRUE)
[1] "Intercept" "Tissue_MCF7_vs_BT474" "Tissue_T47D_vs_BT474"
[4] "Tissue_ZR75_vs_BT474"
>
> #Change design and factor ordering
> tamoxifen <- dba.contrast(tamoxifen,design="~Tissue + Condition",
+ reorderMeta=list(Condition="Responsive",
+ Tissue=c("MCF7","ZR75","T47D","BT474")))
Replacing design.
Computing results names...
> dba.contrast(tamoxifen, bGetCoefficients=TRUE)
[1] "Intercept" "Tissue_ZR75_vs_MCF7"
[3] "Tissue_T47D_vs_MCF7" "Tissue_BT474_vs_MCF7"
[5] "Condition_Resistant_vs_Responsive"
> tamoxifen <- dba.contrast(tamoxifen,contrast="Tissue_BT474_vs_MCF7")
> tamoxifen <- dba.contrast(tamoxifen,contrast=list("Tissue_BT474_vs_MCF7"))
> tamoxifen <- dba.contrast(tamoxifen,contrast=c(0,0,0,1,0))
> tamoxifen <- dba.contrast(tamoxifen,
+ contrast=list("Tissue_BT474_vs_MCF7","Tissue_T47D_vs_MCF7"))
> tamoxifen <- dba.contrast(tamoxifen,contrast=c(0,0,-1,1,0))
> tamoxifen <- dba.contrast(tamoxifen,contrast=c(0,0,0,0,1))
> dba.show(tamoxifen,bContrasts=TRUE)
Factor Group Samples Group2 Samples2
1 Tissue BT474 2 MCF7 5
2 Name Tissue_BT474_vs_MCF7
3 Results Tissue_BT474_vs_MCF7
4 Coefficient 0,0,0,1,0
5 Results Tissue_BT474_vs_MCF7 Tissue_T47D_vs_MCF7
6 Coefficient 0,0,-1,1,0
7 Coefficient 0,0,0,0,1
Intercept Tissue_ZR75_vs_MCF7 Tissue_T47D_vs_MCF7 Tissue_BT474_vs_MCF7
1 0 0 0 1
2 _ _ _ _
3 _ _ _ _
4 0 0 0 1
5 _ _ _ _
6 0 0 -1 1
7 0 0 0 0
Condition_Resistant_vs_Responsive
1 0
2 _
3 _
4 0
5 _
6 0
7 1
> tamoxifen <- dba.analyze(tamoxifen)
Normalize DESeq2 with defaults...
Analyzing...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
> tamoxifen
11 Samples, 2845 sites in matrix:
ID Tissue Factor Condition Treatment Replicate Reads FRiP
1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16
2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15
3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31
4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19
5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25
6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11
7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06
8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22
9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14
10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33
11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22
Design: [~Tissue + Condition] | 7 Contrasts:
Factor Group Samples Group2 Samples2
1 Tissue BT474 2 MCF7 5
2 Name Tissue_BT474_vs_MCF7
3 Results Tissue_BT474_vs_MCF7
4 Coefficient 0,0,0,1,0
5 Results Tissue_BT474_vs_MCF7 Tissue_T47D_vs_MCF7
6 Coefficient 0,0,-1,1,0
7 Coefficient 0,0,0,0,1
Intercept Tissue_ZR75_vs_MCF7 Tissue_T47D_vs_MCF7 Tissue_BT474_vs_MCF7
1 0 0 0 1
2 _ _ _ _
3 _ _ _ _
4 0 0 0 1
5 _ _ _ _
6 0 0 -1 1
7 0 0 0 0
Condition_Resistant_vs_Responsive DB.DESeq2
1 0 988
2 _ 988
3 _ 988
4 0 988
5 _ 1096
6 0 1096
7 1 783
> tamoxifen <- dba.contrast(tamoxifen,
+ contrast=c("Condition","Responsive","Resistant"))
> tamoxifen <- dba.analyze(tamoxifen)
Analyzing...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 947560 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>>> DiffBind 3.12.0
>
> test_check("DiffBind")
* 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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/DiffBind.Rcheck/00check.log’
for details.
DiffBind.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL DiffBind ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘DiffBind’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bamReader.cpp -o bamReader.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c merge.cpp -o merge.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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)
DiffBind.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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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, sort, 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 3.12.0
>
> test_check("DiffBind")
DiffBind.Rcheck/DiffBind-Ex.timings
| name | user | system | elapsed | |
| dba | 1.677 | 0.180 | 1.867 | |
| dba.analyze | 17.502 | 0.809 | 18.466 | |
| dba.blacklist | 9.431 | 0.173 | 9.641 | |