Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:31 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (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 330/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPComp 1.32.0  (landing page)
Li Chen
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/ChIPComp
git_branch: RELEASE_3_18
git_last_commit: 46346bb
git_last_commit_date: 2023-10-24 10:44:51 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for ChIPComp on kunpeng2


To the developers/maintainers of the ChIPComp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPComp.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.

raw results


Summary

Package: ChIPComp
Version: 1.32.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ChIPComp.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ChIPComp_1.32.0.tar.gz
StartedAt: 2023-11-02 09:11:57 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 09:17:27 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 329.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ChIPComp.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ChIPComp.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ChIPComp_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPComp.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 ‘ChIPComp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPComp’ version ‘1.32.0’
* 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 ‘ChIPComp’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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
ChIPComp: no visible global function definition for ‘queryHits’
ChIPComp: no visible global function definition for ‘pnorm’
findCommonPeak: no visible global function definition for ‘ppois’
getCTCounts: no visible global function definition for ‘seqlevels’
getCTCounts: no visible global function definition for ‘seqnames’
getCTCounts: no visible global function definition for ‘subjectHits’
getCTCounts: no visible global function definition for ‘queryHits’
makeConf: no visible global function definition for ‘read.csv’
makeConf: no visible global function definition for ‘model.matrix’
makePeakSet: no visible global function definition for ‘subjectHits’
plot.ChIPComp : mypar: no visible global function definition for ‘par’
plot.ChIPComp: no visible global function definition for ‘lm’
plot.ChIPComp: no visible global function definition for ‘coef’
plot.ChIPComp: no visible global function definition for
  ‘smooth.spline’
plot.ChIPComp: no visible global function definition for ‘lines’
regress: no visible global function definition for ‘lm’
regress: no visible global function definition for ‘coef’
regress: no visible global function definition for ‘resid’
regress: no visible global function definition for ‘smooth.spline’
regress: no visible global function definition for ‘predict’
rmdup: no visible global function definition for ‘qbinom’
Undefined global functions or variables:
  coef lines lm model.matrix par pnorm ppois predict qbinom queryHits
  read.csv resid seqlevels seqnames smooth.spline subjectHits
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "coef", "lm", "model.matrix", "pnorm", "ppois",
             "predict", "qbinom", "resid", "smooth.spline")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) ChIPComp.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) ChIPComp.Rd:28: Escaped LaTeX specials: \# \#
checkRd: (-1) makeCountSet.Rd:56: Escaped LaTeX specials: \# \#
checkRd: (-1) makeCountSet.Rd:57: Escaped LaTeX specials: \# \#
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ChIPComp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeCountSet
> ### Title: make differential binding sites data frame
> ### Aliases: makeCountSet
> 
> ### ** Examples
> 
> 	conf=data.frame(
+ 		SampleID=1:4,
+ 		condition=c("Helas3","Helas3","K562","K562"),
+ 		factor=c("H3k27ac","H3k27ac","H3k27ac","H3k27ac"),
+ 		ipReads=system.file("extdata",c("Helas3.ip1.bed","Helas3.ip2.bed","K562.ip1.bed","K562.ip2.bed"),package="ChIPComp"),
+ 		ctReads=system.file("extdata",c("Helas3.ct.bed","Helas3.ct.bed","K562.ct.bed","K562.ct.bed"),package="ChIPComp"),
+ 		peaks=system.file("extdata",c("Helas3.peak.bed","Helas3.peak.bed","K562.peak.bed","K562.peak.bed"),package="ChIPComp")
+ 	)
> 	conf$condition=factor(conf$condition)
>   conf$factor=factor(conf$factor)
> 	design=as.data.frame(lapply(conf[,c("condition","factor")],as.numeric))-1
> 	design=as.data.frame(model.matrix(~condition,design))
> 	countSet=makeCountSet(conf,design,filetype="bed", species="hg19",binsize=1000)
Making peak list......

Making ip counts......
Making control counts......

* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 507240 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  Attaching package: 'S4Vectors'
  
  The following object is masked from 'package:utils':
  
      findMatches
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Making peak list......
  
  Making ip counts......
  Making control counts......
  
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPComp.Rcheck/00check.log’
for details.


Installation output

ChIPComp.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ChIPComp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘ChIPComp’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c mva.c -o mva.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o ChIPComp.so mva.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-ChIPComp/00new/ChIPComp/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 (ChIPComp)

Tests output

ChIPComp.Rcheck/tests/runTests.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)

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.

> BiocGenerics:::testPackage("ChIPComp")

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


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Making peak list......

Making ip counts......
Making control counts......


Example timings

ChIPComp.Rcheck/ChIPComp-Ex.timings

nameusersystemelapsed
ChIPComp0.0310.0000.046
makeConf0.0090.0000.010