Harmen Bussemaker
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/SELEX |
| Branch: RELEASE_3_7 |
| Last Commit: a045a96 |
| Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:54:18 -0400 (Wed, 17 Oct 2018).
| Package 1337/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SELEX 1.12.0 Harmen Bussemaker
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SELEX |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SELEX_1.12.0.tar.gz |
| StartedAt: 2018-10-16 23:58:39 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-17 00:01:05 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 145.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SELEX.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SELEX_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SELEX.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.12.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SELEX’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
selex.config: no visible global function definition for ‘read.table’
selex.config: no visible global function definition for ‘write.table’
selex.counts: no visible global function definition for ‘flush.console’
selex.infogain: no visible global function definition for
‘flush.console’
selex.kmax: no visible global function definition for ‘flush.console’
selex.loadCountTable: no visible global function definition for
‘flush.console’
selex.mm: no visible global function definition for ‘flush.console’
selex.revcomp: no visible global function definition for
‘complete.cases’
Undefined global functions or variables:
complete.cases flush.console read.table write.table
Consider adding
importFrom("stats", "complete.cases")
importFrom("utils", "flush.console", "read.table", "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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SELEX 35.464 5.767 18.953
selex.seqfilter 11.718 1.413 5.490
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/SELEX.Rcheck/00check.log’
for details.
SELEX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SELEX ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘SELEX’ ... ** 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 (SELEX)
SELEX.Rcheck/SELEX-Ex.timings
| name | user | system | elapsed | |
| SELEX | 35.464 | 5.767 | 18.953 | |
| selex.affinities | 1.295 | 0.372 | 1.328 | |
| selex.config | 0.343 | 0.100 | 0.284 | |
| selex.countSummary | 1.645 | 0.426 | 1.480 | |
| selex.counts | 2.067 | 0.477 | 1.766 | |
| selex.defineSample | 0.264 | 0.103 | 0.300 | |
| selex.exampledata | 0.257 | 0.104 | 0.292 | |
| selex.fastqPSFM | 0.932 | 0.143 | 0.713 | |
| selex.getAttributes | 0.555 | 0.139 | 0.419 | |
| selex.getRound0 | 0.359 | 0.132 | 0.454 | |
| selex.getSeqfilter | 0.877 | 0.118 | 0.306 | |
| selex.infogain | 3.462 | 0.900 | 2.801 | |
| selex.infogainSummary | 0.999 | 0.369 | 1.229 | |
| selex.jvmStatus | 0.196 | 0.092 | 0.281 | |
| selex.kmax | 1.949 | 0.840 | 2.496 | |
| selex.kmerPSFM | 0.912 | 0.251 | 0.836 | |
| selex.loadAnnotation | 0.837 | 0.138 | 0.462 | |
| selex.mm | 1.478 | 0.358 | 1.153 | |
| selex.mmProb | 0.919 | 0.342 | 1.110 | |
| selex.mmSummary | 0.875 | 0.354 | 1.150 | |
| selex.revcomp | 1.394 | 0.389 | 1.443 | |
| selex.run | 3.863 | 0.865 | 2.697 | |
| selex.sample | 0.458 | 0.154 | 0.471 | |
| selex.samplePSFM | 1.181 | 0.158 | 0.865 | |
| selex.sampleSummary | 0.452 | 0.146 | 0.452 | |
| selex.saveAnnotation | 0.248 | 0.136 | 0.387 | |
| selex.seqfilter | 11.718 | 1.413 | 5.490 | |
| selex.setwd | 0.304 | 0.101 | 0.272 | |
| selex.split | 0.750 | 0.308 | 0.970 | |
| selex.summary | 2.270 | 0.837 | 2.718 | |