ampliQueso 1.10.0
Michal Okoniewski
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ampliQueso | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ampliQueso_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ampliQueso.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.10.0’
* 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 ... 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 ‘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 ‘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’
.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 knit makeCluster
p.adjust permp qual ranges read.table readVcf ref registerDoParallel
rowttests seqnames start stopCluster str strand width
Consider adding
importFrom("stats", "aggregate", "end", "p.adjust", "start")
importFrom("utils", "combn", "read.table", "str")
to your NAMESPACE file.
* 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
* 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-3.3-bioc/meat/ampliQueso.Rcheck/00check.log’
for details.