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This page was generated on 2022-01-25 11:10:46 -0500 (Tue, 25 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cTRAP on merida1


To the developers/maintainers of the cTRAP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cTRAP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 431/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.13.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2022-01-24 13:55:18 -0500 (Mon, 24 Jan 2022)
git_url: https://git.bioconductor.org/packages/cTRAP
git_branch: master
git_last_commit: df90b00
git_last_commit_date: 2021-10-26 12:47:45 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'fgsea' which is not available

Summary

Package: cTRAP
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cTRAP_1.13.0.tar.gz
StartedAt: 2022-01-24 23:52:42 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-25 00:07:01 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 858.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cTRAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cTRAP_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cTRAP.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.13.0’
* 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 ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
* checking package 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
taskAsyncApply: no visible global function definition for ‘prepareArgs’
Undefined global functions or variables:
  prepareArgs
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
plotDrugSetEnrichment                    282.498  1.248 284.631
convertGeneIdentifiers                    27.734  1.586  30.987
plot.referenceComparison                  21.985  0.935  22.977
analyseDrugSetEnrichment                  19.761  2.580  32.204
plot.perturbationChanges                  18.355  0.654  19.064
prepareDrugSets                            8.889  3.531  12.462
filterCMapMetadata                         8.472  0.930  25.602
downloadENCODEknockdownMetadata            8.094  0.925  16.982
plotTargetingDrugsVSsimilarPerturbations   8.341  0.413   8.768
predictTargetingDrugs                      6.295  0.326   6.631
prepareCMapPerturbations                   6.076  0.135   6.220
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/cTRAP.Rcheck/00check.log’
for details.



Installation output

cTRAP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cTRAP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘cTRAP’ ...
** 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 (cTRAP)

Tests output

cTRAP.Rcheck/tests/spelling.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.338   0.077   0.392 

cTRAP.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs'
downloaded 31.6 MB

trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs'
downloaded 2.1 MB

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 244 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 244 ]
> 
> proc.time()
   user  system elapsed 
 88.442   7.205  93.798 

Example timings

cTRAP.Rcheck/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment19.761 2.58032.204
convertGeneIdentifiers27.734 1.58630.987
downloadENCODEknockdownMetadata 8.094 0.92516.982
filterCMapMetadata 8.472 0.93025.602
getCMapConditions0.0040.0010.004
getCMapPerturbationTypes0.0000.0000.001
listExpressionDrugSensitivityAssociation0.0000.0010.000
loadCMapData3.8090.2194.389
loadCMapZscores3.0220.1583.183
loadDrugDescriptors0.0680.0100.077
loadENCODEsamples0.0000.0000.001
loadExpressionDrugSensitivityAssociation1.2510.5281.782
parseCMapID0.0010.0000.001
performDifferentialExpression0.0020.0000.002
plot.perturbationChanges18.355 0.65419.064
plot.referenceComparison21.985 0.93522.977
plotDrugSetEnrichment282.498 1.248284.631
plotTargetingDrugsVSsimilarPerturbations8.3410.4138.768
predictTargetingDrugs6.2950.3266.631
prepareCMapPerturbations6.0760.1356.220
prepareDrugSets 8.889 3.53112.462
prepareENCODEgeneExpression0.0010.0000.001
rankSimilarPerturbations2.2050.0852.293