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BioC 3.1: CHECK report for bsseq on zin2

This page was generated on 2015-10-09 09:25:01 -0700 (Fri, 09 Oct 2015).

Package 120/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.4.0
Kasper Daniel Hansen
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/bsseq
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bsseq
Version: 1.4.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_1.4.0.tar.gz
StartedAt: 2015-10-08 22:57:57 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:59:49 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 112.7 seconds
RetCode: 0
Status:  OK 
CheckDir: bsseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/bsseq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘parallel’
  ‘matrixStats’ ‘GenomeInfoDb’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘bsseq’ can be installed ... [11s/11s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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
subsetDmrs: no visible binding for global variable ‘n’
subsetDmrs: no visible binding for global variable ‘meanDiff’
subsetDmrs: no visible binding for global variable ‘invdensity’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/17s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
BSmooth.tstat 5.551  0.152   6.265
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [6s/6s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/bsseq.Rcheck/00check.log’
for details.


bsseq.Rcheck/00install.out:

* installing *source* package ‘bsseq’ ...
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (bsseq)

bsseq.Rcheck/bsseq-Ex.timings:

nameusersystemelapsed
BS.chr220.9090.0120.920
BSmooth0.0010.0000.000
BSmooth.tstat5.5510.1526.265
BSseq-class0.1460.0000.146
BSseq0.0960.0000.096
data.frame2GRanges0.0160.0000.016
dmrFinder1.5840.0081.728
fisherTests0.0660.0000.068
getCoverage0.3200.0120.332
getMeth0.7390.4931.232
getStats0.3900.0080.398
goodnessOfFit1.8470.0162.194
hasGRanges-class0.0020.0000.001
read.bismark0.0000.0000.001
read.umtab0.0000.0040.000