Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-21 11:07:12 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for ChIPComp on riesling1


To the developers/maintainers of the ChIPComp package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 296/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPComp 1.25.0  (landing page)
Li Chen
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChIPComp
git_branch: master
git_last_commit: f8cfac7
git_last_commit_date: 2021-10-26 12:22:08 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPComp
Version: 1.25.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPComp.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPComp_1.25.0.tar.gz
StartedAt: 2022-01-20 18:28:57 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:32:10 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 192.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPComp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPComp.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPComp_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChIPComp.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPComp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPComp' version '1.25.0'
* 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 'ChIPComp' can be installed ... OK
* 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 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 ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/ChIPComp/libs/x64/ChIPComp.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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. 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
makeCountSet 8.69   2.34   11.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/ChIPComp.Rcheck/00check.log'
for details.



Installation output

ChIPComp.Rcheck/00install.out

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChIPComp
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ChIPComp' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c mva.c -o mva.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ChIPComp.dll tmp.def mva.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ChIPComp/00new/ChIPComp/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPComp'
    finding HTML links ... done
    ChIPComp-package                        html  
    ChIPComp                                html  
    makeConf                                html  
    makeCountSet                            html  
    plot                                    html  
    print                                   html  
    seqData                                 html  
** 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 (ChIPComp)
Making 'packages.html' ... done

Tests output

ChIPComp.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Making peak list......

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



RUNIT TEST PROTOCOL -- Thu Jan 20 18:32:01 2022 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPComp RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  14.31    2.95   17.25 

Example timings

ChIPComp.Rcheck/ChIPComp-Ex.timings

nameusersystemelapsed
ChIPComp0.020.000.02
makeConf0.010.000.01
makeCountSet 8.69 2.3411.03
plot0.020.020.03
print0.010.000.02
seqData000