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BioC 3.2: CHECK report for ampliQueso on zin1

This page was generated on 2016-04-23 10:13:23 -0700 (Sat, 23 Apr 2016).

Package 39/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ampliQueso 1.8.0
Michal Okoniewski
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ampliQueso
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ampliQueso
Version: 1.8.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ampliQueso_1.8.0.tar.gz
StartedAt: 2016-04-22 22:04:06 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:07:59 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 232.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ampliQueso.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ampliQueso_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ampliQueso.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ampliQueso/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ampliQueso’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘rnaSeqMap’ ‘knitr’ ‘rgl’ ‘ggplot2’ ‘gplots’ ‘parallel’ ‘doParallel’
  ‘foreach’ ‘VariantAnnotation’ ‘genefilter’ ‘statmod’ ‘xtable’
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 ‘ampliQueso’ can be installed ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘samr’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘VariantAnnotation’ ‘doParallel’ ‘foreach’ ‘genefilter’ ‘ggplot2’
  ‘gplots’ ‘knitr’ ‘parallel’ ‘rgl’ ‘statmod’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘rnaSeqMap:::newSeqReads’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.callCamelTestReg: no visible global function definition for ‘permp’
.callSamPileup: no visible global function definition for ‘readVcf’
.callSamPileup: no visible global function definition for ‘seqnames’
.callSamPileup: no visible global function definition for ‘ranges’
.callSamPileup: no visible global function definition for ‘width’
.callSamPileup: no visible global function definition for ‘ref’
.callSamPileup: no visible global function definition for ‘strand’
.callSamPileup: no visible global function definition for ‘qual’
.camelTest: no visible global function definition for ‘permp’
.camelTestParReg: no visible global function definition for
  ‘makeCluster’
.camelTestParReg: no visible global function definition for
  ‘detectCores’
.camelTestParReg: no visible global function definition for
  ‘registerDoParallel’
.camelTestParReg: no visible global function definition for ‘%dopar%’
.camelTestParReg: no visible global function definition for ‘foreach’
.camelTestParReg: no visible global function definition for
  ‘stopCluster’
.compareCoveragesRegParM: no visible global function definition for
  ‘makeCluster’
.compareCoveragesRegParM: no visible global function definition for
  ‘detectCores’
.compareCoveragesRegParM: no visible global function definition for
  ‘registerDoParallel’
.compareCoveragesRegParM: no visible global function definition for
  ‘%dopar%’
.compareCoveragesRegParM: no visible global function definition for
  ‘foreach’
.compareCoveragesRegParM: no visible global function definition for
  ‘stopCluster’
.compareCoveragesRegParR: no visible global function definition for
  ‘makeCluster’
.compareCoveragesRegParR: no visible global function definition for
  ‘detectCores’
.compareCoveragesRegParR: no visible global function definition for
  ‘registerDoParallel’
.compareCoveragesRegParR: no visible global function definition for
  ‘%dopar%’
.compareCoveragesRegParR: no visible global function definition for
  ‘foreach’
.compareCoveragesRegParR: no visible global function definition for
  ‘stopCluster’
.getSNP: no visible global function definition for ‘readVcf’
.getSNP: no visible global function definition for ‘seqnames’
.getSNP: no visible global function definition for ‘ranges’
.getSNP: no visible global function definition for ‘width’
.getSNP: no visible global function definition for ‘ref’
.getSNP: no visible global function definition for ‘strand’
.getSNP: no visible global function definition for ‘qual’
.getSNPPar: no visible global function definition for ‘makeCluster’
.getSNPPar: no visible global function definition for ‘detectCores’
.getSNPPar: no visible global function definition for
  ‘registerDoParallel’
.getSNPPar: no visible global function definition for ‘%dopar%’
.getSNPPar: no visible global function definition for ‘foreach’
.getSNPPar: no visible global function definition for ‘stopCluster’
runAQReport: no visible global function definition for ‘rowttests’
runAQReport: no visible global function definition for ‘%do%’
runAQReport: no visible global function definition for ‘foreach’
runAQReport: no visible global function definition for ‘knit’
* 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 ... [17s/17s] 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-3.2-bioc/meat/ampliQueso.Rcheck/00check.log’
for details.


ampliQueso.Rcheck/00install.out:

* installing *source* package ‘ampliQueso’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ampliQueso)

ampliQueso.Rcheck/ampliQueso-Ex.timings:

nameusersystemelapsed
camelSampleTable0.0050.0000.005