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CHECK report for ampliQueso on malbec2

This page was generated on 2018-10-29 10:10:32 -0400 (Mon, 29 Oct 2018).

Package 45/1642HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ampliQueso 1.19.4
Michal Okoniewski
Snapshot Date: 2018-10-28 16:46:29 -0400 (Sun, 28 Oct 2018)
URL: https://git.bioconductor.org/packages/ampliQueso
Branch: master
Last Commit: 1e2c703
Last Changed Date: 2018-10-18 08:06:35 -0400 (Thu, 18 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ampliQueso
Version: 1.19.4
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ampliQueso.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ampliQueso_1.19.4.tar.gz
StartedAt: 2018-10-29 00:29:45 -0400 (Mon, 29 Oct 2018)
EndedAt: 2018-10-29 00:34:12 -0400 (Mon, 29 Oct 2018)
EllapsedTime: 266.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ampliQueso.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ampliQueso.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ampliQueso_1.19.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ampliQueso.Rcheck’
* using R Under development (unstable) (2018-10-16 r75448)
* 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 ‘1.19.4’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'ampliQueso' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.9-bioc/meat/ampliQueso.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘BiocManager’
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 ‘hasArg’
.callSamPileup: no visible global function definition for ‘readVcf’
.callSamPileup: no visible global function definition for ‘seqnames’
.callSamPileup: no visible global function definition for ‘start’
.callSamPileup: no visible global function definition for ‘ranges’
.callSamPileup: no visible global function definition for ‘end’
.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 ‘read.table’
.camelTest: no visible binding for global variable ‘str’
.camelTest: no visible global function definition for ‘permp’
.camelTestParReg: no visible global function definition for
  ‘read.table’
.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’
.compareCoveragesRegApply: no visible global function definition for
  ‘read.table’
.compareCoveragesRegParM: no visible global function definition for
  ‘read.table’
.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
  ‘read.table’
.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’
.compareCoveragesRegSeq: no visible global function definition for
  ‘read.table’
.getSNP: no visible global function definition for ‘read.table’
.getSNP: no visible global function definition for ‘hasArg’
.getSNP: no visible global function definition for ‘readVcf’
.getSNP: no visible global function definition for ‘seqnames’
.getSNP: no visible global function definition for ‘start’
.getSNP: no visible global function definition for ‘ranges’
.getSNP: no visible global function definition for ‘end’
.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 ‘read.table’
.getSNPPar: no visible global function definition for ‘%dopar%’
.getSNPPar: no visible global function definition for ‘foreach’
.getSNPPar: no visible global function definition for ‘stopCluster’
.loadLibs: no visible global function definition for ‘install.packages’
.perm.samples: no visible global function definition for ‘combn’
compareCoverages: no visible global function definition for
  ‘read.table’
getCountTable: no visible global function definition for ‘read.table’
runAQReport: no visible global function definition for ‘read.table’
runAQReport: no visible global function definition for ‘rowttests’
runAQReport: no visible global function definition for ‘p.adjust’
runAQReport: no visible global function definition for ‘%do%’
runAQReport: no visible global function definition for ‘foreach’
runAQReport: no visible global function definition for ‘aggregate’
runAQReport: no visible global function definition for ‘knit’
Undefined global functions or variables:
  %do% %dopar% aggregate combn detectCores end foreach hasArg
  install.packages knit makeCluster p.adjust permp qual ranges
  read.table readVcf ref registerDoParallel rowttests seqnames start
  stopCluster str strand width
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "aggregate", "end", "p.adjust", "start")
  importFrom("utils", "combn", "install.packages", "read.table", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.9-bioc/R/library/ampliQueso’, resetting
* 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 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ampliQueso.Rcheck/00check.log’
for details.



Installation output

ampliQueso.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ampliQueso
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ampliQueso’ ...
** 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
Warning: Package 'ampliQueso' is deprecated and will be removed from
  Bioconductor version 3.9
* DONE (ampliQueso)

Tests output


Example timings

ampliQueso.Rcheck/ampliQueso-Ex.timings

nameusersystemelapsed
camelSampleTable0.0030.0000.004
ndMax0.0020.0000.002
ndMin0.0000.0020.002
runAQReport000