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BioC 3.6: CHECK report for REDseq on veracruz1

This page was generated on 2017-08-16 13:41:44 -0400 (Wed, 16 Aug 2017).

Package 1109/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.23.0
Lihua Julie Zhu
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/REDseq
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: REDseq
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings REDseq_1.23.0.tar.gz
StartedAt: 2017-08-16 07:32:26 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 07:37:03 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 277.2 seconds
RetCode: 0
Status:  OK 
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings REDseq_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/REDseq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘REDseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REDseq’ version ‘1.23.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘BSgenome.Celegans.UCSC.ce2’ ‘multtest’ ‘Biostrings’
  ‘BSgenome’ ‘ChIPpeakAnno’
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 ‘REDseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘Biostrings’ ‘ChIPpeakAnno’ ‘multtest’
A package should be listed in only one of these fields.
* 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 ... NOTE
Package in Depends field not imported from: 'BSgenome.Celegans.UCSC.ce2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
buildREmap 5.622  0.172   6.335
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/REDseq.Rcheck/00check.log’
for details.


REDseq.Rcheck/00install.out:

* installing *source* package ‘REDseq’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: %in%, rep.int
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%, rep.int
* DONE (REDseq)

REDseq.Rcheck/REDseq-Ex.timings:

nameusersystemelapsed
REDseq-package0.0140.0010.015
assignSeq2REsite1.9360.0452.306
binom.test.REDseq0.0120.0000.012
buildREmap5.6220.1726.335
compareREDseq0.1700.0000.187
distanceHistSeq2RE0.0280.0020.032
example.REDseq0.0030.0020.004
example.assignedREDseq0.0030.0010.004
example.map0.0020.0010.003
plotCutDistribution0.0280.0030.035
searchPattern2.9720.1313.331
summarizeByRE0.0290.0010.031
summarizeBySeq0.0060.0020.007
writeHits0.0070.0000.007