HTSeqGenie 3.21.0
Jens Reeder
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HTSeqGenie | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings HTSeqGenie_3.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘3.21.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... WARNING
'::' or ':::' import not declared from: ‘BSgenome.Hsapiens.UCSC.hg19’
Unexported objects imported by ':::' calls:
‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’
‘gmapR:::checkPackageInstalled’ ‘gmapR:::geneGenomeName’
‘gmapR:::getDefaultGmapGenomePath’ ‘gmapR:::getGeneRoi’
‘gmapR:::subsetRegion’ ‘parallel:::mckill’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.zipUp: no visible global function definition for ‘bgzip’
AnyGenome: no visible global function definition for
‘GmapGenomeDirectory’
AnyGenome: no visible global function definition for ‘strand<-’
AnyGenome: no visible global function definition for ‘getSeq’
AnyGenome: no visible global function definition for ‘spliceSites<-’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘genome’
buildAnyFastaGenome: no visible global function definition for
‘DNAStringSet’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildAnyFastaGenome: no visible global function definition for
‘indexFa’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘values’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘values<-’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘strand<-’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘strand’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘reduce’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘psetdiff’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘elementLengths’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘ranges’
buildTP53FastaGenome: no visible global function definition for
‘genome’
buildTP53FastaGenome: no visible global function definition for
‘DNAStringSet’
buildTP53FastaGenome: no visible global function definition for
‘getSeq’
buildTP53GenomeTemplate: no visible global function definition for
‘path’
buildTP53GenomeTemplate: no visible global function definition for
‘genome’
buildTallyParam: no visible global function definition for ‘seqlengths’
buildTallyParam: no visible global function definition for ‘seqinfo’
callVariantsGATK: no visible global function definition for
‘indexTabix’
catBams: no visible global function definition for ‘indexBam’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘width’
computeCoverage: no visible global function definition for ‘coverage’
computeCoverage: no visible global function definition for
‘seqlengths<-’
computeCoverage: no visible global function definition for ‘seqlengths’
computeWidth: no visible global function definition for ‘width’
computeWidth: no visible global function definition for ‘reduce’
consolidateByRead: no visible global function definition for
‘elementLengths’
countFeatures : <anonymous>: no visible global function definition for
‘findOverlaps’
countFeatures : <anonymous>: no visible global function definition for
‘queryHits’
countFeatures : <anonymous>: no visible global function definition for
‘queryLength’
countFeatures : <anonymous>: no visible global function definition for
‘subjectHits’
detectQualityInFASTQFile: no visible global function definition for
‘quality’
estimateCutoffs : <anonymous>: no visible global function definition
for ‘mclapply’
excludeVariantsByRegions: no visible global function definition for
‘rowData’
excludeVariantsByRegions: no visible global function definition for
‘findOverlaps’
filterByLength: no visible global function definition for ‘width’
filterGATKVars: no visible global function definition for ‘strand<-’
getAdapterSeqs: no visible global function definition for
‘readDNAStringSet’
getGenomeSegments: no visible global function definition for ‘seqinfo’
getRandomAlignCutoff: no visible binding for global variable
‘DNA_ALPHABET’
getRandomAlignCutoff: no visible global function definition for
‘DNAStringSet’
getRandomAlignCutoff: no visible global function definition for
‘pairwiseAlignment’
hashCoverage : <anonymous>: no visible global function definition for
‘runValue’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for
‘quality’
isAboveQualityThresh: no visible global function definition for
‘BStringSet’
isAboveQualityThresh: no visible global function definition for ‘width’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for ‘Rle’
isAboveQualityThresh: no visible global function definition for
‘viewMeans’
isAdapter: no visible global function definition for
‘pairwiseAlignment’
listIterator.init: no visible binding for '<<-' assignment to
‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
makeRandomSreads: no visible binding for global variable ‘DNA_ALPHABET’
makeRandomSreads: no visible global function definition for
‘DNAStringSet’
makeRandomSreads: no visible global function definition for
‘BStringSet’
markDups: no visible global function definition for ‘indexBam’
mergeBAMsAcrossDirs: no visible global function definition for
‘mclapply’
mergeBams: no visible global function definition for ‘mergeBam’
mergeBams: no visible global function definition for ‘sortBam’
mergeBams: no visible global function definition for ‘indexBam’
mergeCounts: no visible global function definition for ‘elementLengths’
mergeCoverage: no visible global function definition for ‘seqlengths<-’
mergeCoverage: no visible global function definition for ‘seqlengths’
plotDepthByStrand: no visible global function definition for ‘values’
preprocessReadsChunk: no visible global function definition for ‘width’
preprocessReadsChunk : <anonymous>: no visible global function
definition for ‘width’
readRNASeqEnds: no visible global function definition for ‘values’
readRNASeqEnds: no visible global function definition for ‘grglist’
readRNASeqEnds: no visible global function definition for ‘strand<-’
readRNASeqEnds: no visible global function definition for ‘values<-’
readRNASeqEnds: no visible global function definition for
‘elementLengths’
safeExecute: no visible global function definition for ‘mccollect’
saveCoverage: no visible global function definition for ‘seqlengths’
sclapply : cleanup: no visible global function definition for
‘mccollect’
sclapply: no visible global function definition for ‘mccollect’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
truncateReads: no visible global function definition for ‘width’
truncateReads: no visible global function definition for ‘subseq’
truncateReads: no visible global function definition for ‘quality’
vcfStat: no visible global function definition for ‘width’
wrapGsnap: no visible global function definition for ‘mclapply’
wrapGsnap : <anonymous>: no visible global function definition for
‘asBam’
writeToFile: no visible binding for global variable ‘logging.file’
writeVCF: no visible global function definition for ‘bgzip’
writeVCF: no visible global function definition for ‘indexTabix’
Undefined global functions or variables:
BStringSet DNAStringSet DNA_ALPHABET GmapGenomeDirectory Rle Views
asBam bgzip coverage elementLengths findOverlaps gaps genome getSeq
grglist indexBam indexFa indexTabix logging.file logging.handlers
logging.loglevel mccollect mclapply mergeBam pairwiseAlignment path
psetdiff quality queryHits queryLength ranges readDNAStringSet reduce
resize rowData runValue seqinfo seqlengths seqlengths<- sortBam
spliceSites<- strand strand<- subjectHits subseq values values<-
viewMeans width
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’ [172s/233s]
[172s/233s] 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: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.
* installing *source* package ‘HTSeqGenie’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: %in%
No methods found in "IRanges" for requests: as.factor
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%
No methods found in "IRanges" for requests: as.factor
* DONE (HTSeqGenie)