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CHECK report for ChIPComp on merida2

This page was generated on 2018-10-17 08:55:14 -0400 (Wed, 17 Oct 2018).

Package 228/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPComp 1.10.0
Li Chen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChIPComp
Branch: RELEASE_3_7
Last Commit: 462b008
Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPComp
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPComp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPComp_1.10.0.tar.gz
StartedAt: 2018-10-16 20:23:24 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:27:24 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 239.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPComp.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPComp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPComp_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPComp.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPComp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPComp’ version ‘1.10.0’
* 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
* 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 ‘plot’
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 plot pnorm ppois predict qbinom
  queryHits read.csv resid seqlevels seqnames smooth.spline subjectHits
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
makeCountSet 10.611   0.99  11.736
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPComp.Rcheck/00check.log’
for details.



Installation output

ChIPComp.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPComp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ChIPComp’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mva.c -o mva.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ChIPComp.so mva.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (ChIPComp)

Tests output

ChIPComp.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Making peak list......

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



RUNIT TEST PROTOCOL -- Tue Oct 16 20:27:19 2018 
*********************************************** 
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 
 21.052   1.548  22.820 

Example timings

ChIPComp.Rcheck/ChIPComp-Ex.timings

nameusersystemelapsed
ChIPComp0.0410.0040.046
makeConf0.0150.0010.016
makeCountSet10.611 0.99011.736
plot0.0450.0020.048
print0.0250.0030.027
seqData0.0030.0010.005