Yue Li
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RIPSeeker |
| Branch: RELEASE_3_8 |
| Last Commit: 3b3bdfa |
| Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
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 |
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### Running command:
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### /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
###
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* 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 | |