Harmen Bussemaker
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SELEX |
| Branch: master |
| Last Commit: fd16eaa |
| Last Changed Date: 2018-10-30 11:54:34 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:13:30 -0400 (Tue, 09 Apr 2019).
| Package 1454/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SELEX 1.15.0 Harmen Bussemaker
| 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: SELEX |
| Version: 1.15.0 |
| 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_1.15.0.tar.gz |
| StartedAt: 2019-04-09 05:21:25 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:25:11 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 225.8 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_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SELEX.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.15.0’
* 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 51.390 15.529 37.854
selex.seqfilter 14.407 3.270 9.379
selex.infogain 5.488 2.448 6.191
selex.run 5.475 2.233 5.547
selex.kmax 3.639 2.202 5.337
selex.summary 3.593 2.042 5.358
* 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘SELEX’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SELEX)
SELEX.Rcheck/SELEX-Ex.timings
| name | user | system | elapsed | |
| SELEX | 51.390 | 15.529 | 37.854 | |
| selex.affinities | 1.970 | 0.971 | 2.579 | |
| selex.config | 0.525 | 0.262 | 0.604 | |
| selex.countSummary | 2.716 | 1.113 | 2.939 | |
| selex.counts | 3.138 | 1.264 | 3.493 | |
| selex.defineSample | 0.459 | 0.278 | 0.659 | |
| selex.exampledata | 0.425 | 0.260 | 0.618 | |
| selex.fastqPSFM | 0.990 | 0.347 | 1.093 | |
| selex.getAttributes | 0.760 | 0.346 | 0.842 | |
| selex.getRound0 | 0.609 | 0.352 | 0.931 | |
| selex.getSeqfilter | 1.564 | 0.284 | 0.933 | |
| selex.infogain | 5.488 | 2.448 | 6.191 | |
| selex.infogainSummary | 1.702 | 0.977 | 2.535 | |
| selex.jvmStatus | 0.418 | 0.271 | 0.685 | |
| selex.kmax | 3.639 | 2.202 | 5.337 | |
| selex.kmerPSFM | 1.300 | 0.627 | 1.626 | |
| selex.loadAnnotation | 1.435 | 0.397 | 0.992 | |
| selex.mm | 1.795 | 0.881 | 2.302 | |
| selex.mmProb | 1.389 | 0.821 | 2.116 | |
| selex.mmSummary | 1.725 | 0.954 | 2.430 | |
| selex.revcomp | 1.960 | 0.996 | 2.709 | |
| selex.run | 5.475 | 2.233 | 5.547 | |
| selex.sample | 0.613 | 0.302 | 0.773 | |
| selex.samplePSFM | 0.859 | 0.346 | 0.992 | |
| selex.sampleSummary | 0.880 | 0.360 | 0.896 | |
| selex.saveAnnotation | 0.442 | 0.311 | 0.751 | |
| selex.seqfilter | 14.407 | 3.270 | 9.379 | |
| selex.setwd | 0.369 | 0.194 | 0.461 | |
| selex.split | 1.448 | 0.791 | 1.987 | |
| selex.summary | 3.593 | 2.042 | 5.358 | |