Nuno Saraiva-Agostinho
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/cTRAP |
| Branch: RELEASE_3_10 |
| Last Commit: 17ddee4 |
| Last Changed Date: 2019-10-29 13:11:25 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:14:54 -0400 (Wed, 15 Apr 2020).
| Package 391/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cTRAP 1.4.0 Nuno Saraiva-Agostinho
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cTRAP |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings cTRAP_1.4.0.tar.gz |
| StartedAt: 2020-04-15 06:06:26 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:17:54 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 687.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cTRAP.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings cTRAP_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/cTRAP.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘cTRAP’ 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 ... OK
* 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 ... NOTE
Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotDrugSetEnrichment 325.552 1.632 109.488
analyseDrugSetEnrichment 289.948 2.264 75.081
predictTargetingDrugs 269.680 1.584 61.007
downloadENCODEknockdownMetadata 65.916 0.520 27.865
plot.perturbationChanges 55.128 0.280 24.834
plot.referenceComparison 44.936 0.252 11.667
rankSimilarPerturbations 34.516 0.228 8.995
loadCMapData 7.668 0.436 7.837
* 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-3.10-bioc/meat/cTRAP.Rcheck/00check.log’
for details.
cTRAP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL cTRAP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘cTRAP’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (cTRAP)
cTRAP.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(testthat)
> library(cTRAP)
>
> test_check("cTRAP")
trying URL 'https://www.dropbox.com/s/5q0dazbtnpojw2m/expressionDrugSensitivityCorGDSC7.rds?raw=1'
Content type 'application/octet-stream' length 36160847 bytes (34.5 MB)
==================================================
downloaded 34.5 MB
trying URL 'https://www.dropbox.com/s/599ok2w9ahysdga/compound_descriptors_NCI60_2D.rds?raw=1'
Content type 'application/octet-stream' length 1616106 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 155 | SKIPPED: 1 | WARNINGS: 10 | FAILED: 0 ]
>
> proc.time()
user system elapsed
861.016 6.492 219.021
cTRAP.Rcheck/cTRAP-Ex.timings
| name | user | system | elapsed | |
| analyseDrugSetEnrichment | 289.948 | 2.264 | 75.081 | |
| downloadENCODEknockdownMetadata | 65.916 | 0.520 | 27.865 | |
| filterCMapMetadata | 0.208 | 0.004 | 0.047 | |
| getCMapConditions | 0.004 | 0.000 | 0.002 | |
| getCMapPerturbationTypes | 0.000 | 0.000 | 0.001 | |
| loadCMapData | 7.668 | 0.436 | 7.837 | |
| loadCMapZscores | 0.004 | 0.000 | 0.000 | |
| loadDrugDescriptors | 2.056 | 0.020 | 0.621 | |
| loadENCODEsamples | 0.004 | 0.000 | 0.001 | |
| loadExpressionDrugSensitivityAssociation | 2.008 | 0.264 | 2.281 | |
| parseCMapID | 0.000 | 0.000 | 0.001 | |
| performDifferentialExpression | 0.004 | 0.000 | 0.002 | |
| plot.perturbationChanges | 55.128 | 0.280 | 24.834 | |
| plot.referenceComparison | 44.936 | 0.252 | 11.667 | |
| plotDrugSetEnrichment | 325.552 | 1.632 | 109.488 | |
| predictTargetingDrugs | 269.680 | 1.584 | 61.007 | |
| prepareCMapPerturbations | 0 | 0 | 0 | |
| prepareDrugSets | 1.792 | 0.572 | 1.594 | |
| prepareENCODEgeneExpression | 0 | 0 | 0 | |
| rankSimilarPerturbations | 34.516 | 0.228 | 8.995 | |