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CHECK report for fCCAC on malbec2

This page was generated on 2019-10-16 12:09:59 -0400 (Wed, 16 Oct 2019).

Package 541/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCCAC 1.10.0
Pedro Madrigal
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/fCCAC
Branch: RELEASE_3_9
Last Commit: e5fc5e4
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: fCCAC
Version: 1.10.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:fCCAC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings fCCAC_1.10.0.tar.gz
StartedAt: 2019-10-16 01:36:30 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:40:41 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 251.0 seconds
RetCode: 0
Status:  OK 
CheckDir: fCCAC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:fCCAC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings fCCAC_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/fCCAC.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fCCAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fCCAC’ 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 ‘fCCAC’ 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
fccac: no visible binding for global variable ‘variables’
Undefined global functions or variables:
  variables
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/fCCAC.Rcheck/00check.log’
for details.



Installation output

fCCAC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL fCCAC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘fCCAC’ ...
** using staged installation
** R
** 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 (fCCAC)

Tests output

fCCAC.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> require("fCCAC") || stop("unable to load fCCAC")
Loading required package: fCCAC
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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, 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, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
[1] TRUE
> BiocGenerics:::testPackage("fCCAC")
[1] "Reading peaks..."
[1] "Starting fCCAC..."
[1] "Reading bigWig file...1/3"
[1] "Reading bigWig file...2/3"
[1] "Reading bigWig file...3/3"
[1] "Performing fCCA in pair...1/3"
[1] "H3K4me3_Rep1...vs...H3K4me3_Rep2"
[1] "Performing fCCA in pair...2/3"
[1] "H3K4me3_Rep1...vs...H3K4me3_Rep3"
[1] "Performing fCCA in pair...3/3"
[1] "H3K4me3_Rep2...vs...H3K4me3_Rep3"
[1] "Reading peaks..."
[1] "Reading peaks..."
[1] "Starting fCCAC..."
[1] "Reading peaks..."
[1] "Starting fCCAC..."


RUNIT TEST PROTOCOL -- Wed Oct 16 01:40:38 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
fCCAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.228   0.534  13.775 

Example timings

fCCAC.Rcheck/fCCAC-Ex.timings

nameusersystemelapsed
fCCAC-internal1.1060.0041.110
fCCAC-package3.2350.0873.349
fccac1.6920.0161.712
heatmapfCCAC1.2380.0051.245