Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:30:42 -0400 (Tue, 09 Apr 2019).
Package 1322/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
REDseq 1.29.0 Lihua Julie Zhu
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: REDseq |
Version: 1.29.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings REDseq_1.29.0.tar.gz |
StartedAt: 2019-04-09 03:07:39 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 03:12:28 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 288.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: REDseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings REDseq_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/REDseq.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘REDseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘REDseq’ version ‘1.29.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'BSgenome.Celegans.UCSC.ce2', 'multtest', 'Biostrings', 'BSgenome', 'ChIPpeakAnno' 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 ‘REDseq’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocGenerics’ ‘Biostrings’ ‘ChIPpeakAnno’ ‘multtest’ A package should be listed in only one of these fields. * 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 Package in Depends field not imported from: 'BSgenome.Celegans.UCSC.ce2' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed buildREmap 9.12 0.128 9.727 * 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-3.9-bioc/meat/REDseq.Rcheck/00check.log’ for details.
REDseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL REDseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘REDseq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq' ** testing if installed package can be loaded from final location No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq' ** testing if installed package keeps a record of temporary installation path * DONE (REDseq)
REDseq.Rcheck/REDseq-Ex.timings
name | user | system | elapsed | |
REDseq-package | 0.007 | 0.000 | 0.007 | |
assignSeq2REsite | 0.979 | 0.068 | 1.048 | |
binom.test.REDseq | 0.014 | 0.000 | 0.014 | |
buildREmap | 9.120 | 0.128 | 9.727 | |
compareREDseq | 0.022 | 0.000 | 0.022 | |
distanceHistSeq2RE | 0.035 | 0.000 | 0.035 | |
example.REDseq | 0.000 | 0.002 | 0.003 | |
example.assignedREDseq | 0.000 | 0.003 | 0.002 | |
example.map | 0.002 | 0.001 | 0.003 | |
plotCutDistribution | 0.036 | 0.004 | 0.040 | |
searchPattern | 3.046 | 0.044 | 3.092 | |
summarizeByRE | 0.006 | 0.000 | 0.006 | |
summarizeBySeq | 0.003 | 0.004 | 0.008 | |
writeHits | 0.008 | 0.000 | 0.007 | |