Richard Cotton
| Snapshot Date: 2019-07-04 17:01:44 -0400 (Thu, 04 Jul 2019) |
| URL: https://git.bioconductor.org/packages/readat |
| Branch: RELEASE_3_9 |
| Last Commit: 097758c |
| Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-07-05 11:58:28 -0400 (Fri, 05 Jul 2019).
| Package 1341/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| readat 1.10.0 Richard Cotton
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: readat |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:readat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings readat_1.10.0.tar.gz |
| StartedAt: 2019-07-05 04:16:58 -0400 (Fri, 05 Jul 2019) |
| EndedAt: 2019-07-05 04:21:18 -0400 (Fri, 05 Jul 2019) |
| EllapsedTime: 260.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: readat.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:readat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings readat_1.10.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/readat.Rcheck’
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘readat/DESCRIPTION’ ... OK
* this is package ‘readat’ version ‘1.10.0’
* 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 ‘readat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
sfread: no visible binding for global variable ‘header’
sfread: no visible binding for global variable ‘nrows’
Undefined global functions or variables:
header nrows
* 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
WideSomaLogicDataAttributes 44.325 0.243 13.113
sub-.WideSomaLogicData 37.454 0.333 7.237
colnamesStartWithSeqId 36.215 0.154 6.636
readAdat 35.237 0.138 6.316
as.SummarizedExperiment 34.662 0.165 9.227
as.ExpressionSet 29.491 0.179 9.763
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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 NOTE
See
‘/home/biocbuild/bbs-3.9-bioc/meat/readat.Rcheck/00check.log’
for details.
readat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL readat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘readat’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (readat)
readat.Rcheck/tests/testthat.Rout
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(readat)
> library(testthat)
>
> test_check("readat")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 62 SKIPPED: 0 WARNINGS: 0 FAILED: 0
>
> proc.time()
user system elapsed
152.494 0.989 33.344
readat.Rcheck/readat-Ex.timings
| name | user | system | elapsed | |
| WideSomaLogicData | 0.016 | 0.008 | 0.024 | |
| WideSomaLogicDataAttributes | 44.325 | 0.243 | 13.113 | |
| aptamers | 0.039 | 0.004 | 0.043 | |
| as.ExpressionSet | 29.491 | 0.179 | 9.763 | |
| as.SummarizedExperiment | 34.662 | 0.165 | 9.227 | |
| chromosomalPositions | 0.112 | 0.000 | 0.113 | |
| colnamesStartWithSeqId | 36.215 | 0.154 | 6.636 | |
| convertSeqIdToAptamer | 0 | 0 | 0 | |
| ensemblIds | 0.002 | 0.000 | 0.002 | |
| extractSampleData | 0.003 | 0.004 | 0.007 | |
| getChromosomalPositions | 0.035 | 0.000 | 0.035 | |
| getEnsemblIds | 0.002 | 0.000 | 0.003 | |
| getGoMolecularFunctions | 0.162 | 0.008 | 0.170 | |
| getKeggDefinitions | 0.019 | 0.000 | 0.019 | |
| getPfam | 0.008 | 0.000 | 0.008 | |
| getUniProtKeywords | 0.014 | 0.000 | 0.014 | |
| goMolecularFunction | 0.170 | 0.008 | 0.178 | |
| keggDefinitions | 0.029 | 0.008 | 0.036 | |
| pfam | 0.009 | 0.000 | 0.009 | |
| readAdat | 35.237 | 0.138 | 6.316 | |
| readComments | 0.096 | 0.008 | 0.038 | |
| readControls | 0.249 | 0.000 | 0.181 | |
| readSamples | 0.342 | 0.000 | 0.280 | |
| readSlides | 0.097 | 0.000 | 0.048 | |
| sub-.WideSomaLogicData | 37.454 | 0.333 | 7.237 | |
| uniprotKeywords | 0.05 | 0.00 | 0.05 | |
| writeSampleSubmissionForm | 0.367 | 0.000 | 0.108 | |