Harmen Bussemaker
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SELEX |
| Branch: RELEASE_3_8 |
| Last Commit: 00b9541 |
| Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:21 -0400 (Tue, 16 Apr 2019).
| Package 1410/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SELEX 1.14.0 Harmen Bussemaker
| 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: SELEX |
| Version: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2019-04-16 02:40:38 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:43:11 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 153.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SELEX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SELEX.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.0’
* 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 37.602 6.101 19.916
selex.seqfilter 12.830 1.411 5.691
selex.run 4.918 0.930 2.918
* 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-3.8-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 | 37.602 | 6.101 | 19.916 | |
| selex.affinities | 1.347 | 0.396 | 1.374 | |
| selex.config | 0.393 | 0.097 | 0.285 | |
| selex.countSummary | 1.647 | 0.405 | 1.439 | |
| selex.counts | 1.998 | 0.486 | 1.729 | |
| selex.defineSample | 0.245 | 0.098 | 0.290 | |
| selex.exampledata | 0.231 | 0.115 | 0.318 | |
| selex.fastqPSFM | 0.887 | 0.151 | 0.707 | |
| selex.getAttributes | 0.575 | 0.141 | 0.435 | |
| selex.getRound0 | 0.377 | 0.153 | 0.513 | |
| selex.getSeqfilter | 0.914 | 0.121 | 0.318 | |
| selex.infogain | 2.870 | 0.953 | 3.030 | |
| selex.infogainSummary | 1.720 | 0.399 | 1.299 | |
| selex.jvmStatus | 0.506 | 0.109 | 0.314 | |
| selex.kmax | 2.009 | 0.869 | 2.571 | |
| selex.kmerPSFM | 0.927 | 0.259 | 0.866 | |
| selex.loadAnnotation | 0.822 | 0.148 | 0.487 | |
| selex.mm | 1.483 | 0.356 | 1.166 | |
| selex.mmProb | 0.960 | 0.340 | 1.145 | |
| selex.mmSummary | 0.920 | 0.347 | 1.143 | |
| selex.revcomp | 1.417 | 0.386 | 1.433 | |
| selex.run | 4.918 | 0.930 | 2.918 | |
| selex.sample | 0.433 | 0.134 | 0.432 | |
| selex.samplePSFM | 0.605 | 0.144 | 0.578 | |
| selex.sampleSummary | 0.439 | 0.141 | 0.445 | |
| selex.saveAnnotation | 0.253 | 0.140 | 0.394 | |
| selex.seqfilter | 12.830 | 1.411 | 5.691 | |
| selex.setwd | 0.562 | 0.112 | 0.297 | |
| selex.split | 1.398 | 0.324 | 0.997 | |
| selex.summary | 2.319 | 0.848 | 2.810 | |