Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:49:48 -0400 (Tue, 16 Apr 2019).
Package 1314/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
RIPSeeker 1.22.0 Yue Li
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: RIPSeeker |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RIPSeeker.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RIPSeeker_1.22.0.tar.gz |
StartedAt: 2019-04-16 02:38:50 -0400 (Tue, 16 Apr 2019) |
EndedAt: 2019-04-16 02:42:39 -0400 (Tue, 16 Apr 2019) |
EllapsedTime: 228.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RIPSeeker.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RIPSeeker.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RIPSeeker_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RIPSeeker.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RIPSeeker/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RIPSeeker’ version ‘1.22.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Rsamtools’ ‘GenomicAlignments’ ‘rtracklayer’ 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 ‘RIPSeeker’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 ... NOTE 'library' or 'require' call to ‘Rsamtools’ which was already attached by Depends. Please remove these calls from your code. 'library' or 'require' calls in package code: ‘ChIPpeakAnno’ ‘GenomicFeatures’ ‘biomaRt’ ‘parallel’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE annotateRIP: no visible global function definition for ‘getAnnotation’ annotateRIP: no visible global function definition for ‘getBM’ annotateRIP: no visible global function definition for ‘write.table’ binCount: no visible global function definition for ‘seqlengths’ combineRIP: no visible global function definition for ‘seqlengths<-’ combineRIP: no visible global function definition for ‘seqlengths’ computeRPKM: no visible global function definition for ‘exonsBy’ computeRPKM: no visible global function definition for ‘cdsBy’ computeRPKM: no visible global function definition for ‘intronsByTranscript’ computeRPKM: no visible global function definition for ‘fiveUTRsByTranscript’ computeRPKM: no visible global function definition for ‘threeUTRsByTranscript’ computeRPKM: no visible global function definition for ‘seqlevels<-’ computeRPKM: no visible global function definition for ‘seqlevels’ computeRPKM: no visible global function definition for ‘read.delim’ computeRPKM: no visible global function definition for ‘getBM’ exportGRanges: no visible global function definition for ‘write.table’ galp2gal: no visible global function definition for ‘seqlengths’ getAlignGal: no visible global function definition for ‘seqlengths<-’ getAlignGal: no visible global function definition for ‘seqlengths’ mainSeek: no visible global function definition for ‘mclapply’ mainSeekSingleChrom: no visible global function definition for ‘seqlengths’ plotCoverage: no visible global function definition for ‘seqlengths’ ripSeek: no visible global function definition for ‘as.roman’ ripSeek: no visible global function definition for ‘write.table’ rulebaseRIPSeek: no visible global function definition for ‘getBM’ rulebaseRIPSeek: no visible global function definition for ‘write.table’ selectBinSize: no visible global function definition for ‘seqlengths’ viewRIP: no visible global function definition for ‘GRangesForUCSCGenome’ Undefined global functions or variables: GRangesForUCSCGenome as.roman cdsBy exonsBy fiveUTRsByTranscript getAnnotation getBM intronsByTranscript mclapply read.delim seqlengths seqlengths<- seqlevels seqlevels<- threeUTRsByTranscript write.table Consider adding importFrom("utils", "as.roman", "read.delim", "write.table") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed mainSeek 16.156 0.004 16.181 disambiguateMultihits 14.844 0.000 14.858 combineRIP 1.456 0.028 16.330 * 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 NOTEs See ‘/home/biocbuild/bbs-3.8-bioc/meat/RIPSeeker.Rcheck/00check.log’ for details.
RIPSeeker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RIPSeeker ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘RIPSeeker’ ... ** R ** 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 * DONE (RIPSeeker)
RIPSeeker.Rcheck/RIPSeeker-Ex.timings
name | user | system | elapsed | |
RIPSeeker-package | 0.004 | 0.000 | 0.000 | |
addDummyProb | 0.652 | 0.000 | 0.675 | |
addPseudoAlignment | 0.944 | 0.000 | 0.946 | |
annotateRIP | 0.012 | 0.000 | 0.010 | |
binCount | 0.452 | 0.016 | 0.467 | |
combineAlignGals | 0.220 | 0.000 | 0.268 | |
combineRIP | 1.456 | 0.028 | 16.330 | |
computeLogOdd | 1.284 | 0.012 | 1.296 | |
computeRPKM | 0.000 | 0.000 | 0.001 | |
disambiguateMultihits | 14.844 | 0.000 | 14.858 | |
empiricalFDR | 0.000 | 0.000 | 0.001 | |
evalBinSize | 0.432 | 0.008 | 0.438 | |
exportGRanges | 0.000 | 0.000 | 0.001 | |
galp2gal | 0.272 | 0.000 | 0.272 | |
getAlignGal | 0.140 | 0.012 | 0.155 | |
logScoreWithControl | 0.004 | 0.000 | 0.006 | |
logScoreWithoutControl | 0.004 | 0.000 | 0.003 | |
mainSeek | 16.156 | 0.004 | 16.181 | |
mainSeekSingleChrom | 1.640 | 0.004 | 1.661 | |
nbh.GRanges | 0 | 0 | 0 | |
nbh | 2.092 | 0.012 | 2.109 | |
nbh.integer | 0 | 0 | 0 | |
nbh_chk | 0 | 0 | 0 | |
nbh_em | 0.332 | 0.000 | 0.331 | |
nbh_gen | 0.004 | 0.000 | 0.003 | |
nbh_init | 1.292 | 0.000 | 1.290 | |
nbh_vit | 0.192 | 0.004 | 0.194 | |
nbm_chk | 0 | 0 | 0 | |
nbm_em | 0.448 | 0.000 | 0.447 | |
plotCoverage | 0.776 | 0.036 | 0.813 | |
plotStrandedCoverage | 1.120 | 0.020 | 1.142 | |
randindx | 0.144 | 0.008 | 0.152 | |
ripSeek | 0.004 | 0.000 | 0.004 | |
rulebaseRIPSeek | 0.004 | 0.000 | 0.001 | |
scoreMergedBins | 0.004 | 0.000 | 0.006 | |
seekRIP | 0.004 | 0.000 | 0.003 | |
selectBinSize | 2.424 | 0.048 | 2.474 | |
statdis | 0.268 | 0.004 | 0.272 | |
viewRIP | 0.004 | 0.000 | 0.003 | |