ampliQueso 1.7.0
Michal Okoniewski
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ampliQueso | | Last Changed Rev: 102594 / Revision: 107696 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ampliQueso_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ampliQueso.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 ‘ampliQueso/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ampliQueso’ version ‘1.7.0’
* 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 ... [19s/20s] 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 ... [16s/16s] 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.