Harmen Bussemaker
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/SELEX |
| Branch: master |
| Last Commit: 20dbc4b |
| Last Changed Date: 2019-11-18 09:01:39 -0500 (Mon, 18 Nov 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:41:26 -0500 (Thu, 16 Jan 2020).
| Package 1550/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Harmen Bussemaker
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: SELEX |
| Version: 1.19.1 |
| 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_1.19.1.tar.gz |
| StartedAt: 2020-01-16 08:44:13 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 08:48:13 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 239.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SELEX.Rcheck |
| Warnings: 1 |
##############################################################################
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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_1.19.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SELEX.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.19.1’
* 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 ... WARNING
Found the following significant warnings:
Warning: Package 'SELEX' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/SELEX.Rcheck/00install.out’ for details.
* 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 (user + system) or elapsed time > 5s
user system elapsed
SELEX 50.673 14.880 36.173
selex.seqfilter 15.194 3.643 10.152
selex.infogain 6.185 2.573 6.433
selex.run 5.142 2.131 5.371
selex.kmax 3.695 2.367 5.683
selex.summary 3.577 2.038 5.322
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-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/4.0/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 Warning: Package 'SELEX' is deprecated and will be removed from Bioconductor version 3.12 ** testing if installed package can be loaded from final location Warning: Package 'SELEX' is deprecated and will be removed from Bioconductor version 3.12 ** testing if installed package keeps a record of temporary installation path * DONE (SELEX)
SELEX.Rcheck/SELEX-Ex.timings
| name | user | system | elapsed | |
| SELEX | 50.673 | 14.880 | 36.173 | |
| selex.affinities | 2.571 | 1.147 | 3.030 | |
| selex.config | 0.560 | 0.346 | 0.739 | |
| selex.countSummary | 2.902 | 1.169 | 2.973 | |
| selex.counts | 3.598 | 1.309 | 3.681 | |
| selex.defineSample | 0.527 | 0.324 | 0.726 | |
| selex.exampledata | 0.405 | 0.275 | 0.649 | |
| selex.fastqPSFM | 1.215 | 0.461 | 1.385 | |
| selex.getAttributes | 0.545 | 0.332 | 0.817 | |
| selex.getRound0 | 0.944 | 0.412 | 1.051 | |
| selex.getSeqfilter | 0.816 | 0.260 | 0.605 | |
| selex.infogain | 6.185 | 2.573 | 6.433 | |
| selex.infogainSummary | 1.692 | 0.957 | 2.510 | |
| selex.jvmStatus | 0.439 | 0.283 | 0.697 | |
| selex.kmax | 3.695 | 2.367 | 5.683 | |
| selex.kmerPSFM | 1.261 | 0.676 | 1.744 | |
| selex.loadAnnotation | 0.693 | 0.379 | 1.021 | |
| selex.mm | 2.464 | 0.902 | 2.377 | |
| selex.mmProb | 1.983 | 0.947 | 2.440 | |
| selex.mmSummary | 1.729 | 0.964 | 2.530 | |
| selex.revcomp | 2.112 | 1.092 | 2.884 | |
| selex.run | 5.142 | 2.131 | 5.371 | |
| selex.sample | 0.613 | 0.384 | 0.987 | |
| selex.samplePSFM | 0.999 | 0.398 | 1.161 | |
| selex.sampleSummary | 0.884 | 0.341 | 0.833 | |
| selex.saveAnnotation | 0.441 | 0.313 | 0.739 | |
| selex.seqfilter | 15.194 | 3.643 | 10.152 | |
| selex.setwd | 0.414 | 0.262 | 0.609 | |
| selex.split | 1.739 | 0.888 | 2.167 | |
| selex.summary | 3.577 | 2.038 | 5.322 | |