HTSeqGenie 3.18.0
Jens Reeder
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/HTSeqGenie | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings HTSeqGenie_3.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/HTSeqGenie.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 ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘3.18.0’
* 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 ... [22s/34s] 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’ [154s/282s]
[154s/282s] 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-3.1-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.
* installing *source* package ‘HTSeqGenie’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "IRanges" for requests: %in%
No methods found in "IRanges" for requests: as.factor
* DONE (HTSeqGenie)