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This page was generated on 2021-06-17 02:38:17 -0400 (Thu, 17 Jun 2021).

CHECK results for cTRAP on nebbiolo1

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 422/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.10.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/cTRAP
Branch: RELEASE_3_13
Last Commit: e21b1e6
Last Changed Date: 2021-05-19 12:39:02 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cTRAP
Version: 1.10.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cTRAP_1.10.0.tar.gz
StartedAt: 2021-06-15 11:29:46 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 11:38:32 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 526.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cTRAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cTRAP_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cTRAP.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.10.0’
* 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 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 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                    123.644  1.183 124.824
plot.referenceComparison                  13.963  0.569  14.532
analyseDrugSetEnrichment                  12.532  1.536  42.616
plot.perturbationChanges                  11.647  0.608  12.256
prepareDrugSets                            5.536  6.243  11.767
filterCMapMetadata                         7.037  1.096   8.606
plotTargetingDrugsVSsimilarPerturbations   5.386  0.160   5.548
prepareCMapPerturbations                   5.037  0.116   4.156
convertENSEMBLtoGeneSymbols                2.371  0.199  12.173
downloadENCODEknockdownMetadata            1.353  0.245  33.269
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/cTRAP.Rcheck/00check.log’
for details.



Installation output

cTRAP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cTRAP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.148   0.035   0.167 

cTRAP.Rcheck/tests/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 1616781 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 244 ]
> 
> proc.time()
   user  system elapsed 
 55.172   3.487  85.615 

Example timings

cTRAP.Rcheck/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment12.532 1.53642.616
convertENSEMBLtoGeneSymbols 2.371 0.19912.173
downloadENCODEknockdownMetadata 1.353 0.24533.269
filterCMapMetadata7.0371.0968.606
getCMapConditions0.0000.0030.003
getCMapPerturbationTypes0.0010.0000.000
listExpressionDrugSensitivityAssociation0.0000.0010.000
loadCMapData3.2440.2143.073
loadCMapZscores2.4310.0701.590
loadDrugDescriptors0.1310.0040.122
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation1.3350.8362.171
parseCMapID0.0010.0000.000
performDifferentialExpression0.0010.0000.001
plot.perturbationChanges11.647 0.60812.256
plot.referenceComparison13.963 0.56914.532
plotDrugSetEnrichment123.644 1.183124.824
plotTargetingDrugsVSsimilarPerturbations5.3860.1605.548
predictTargetingDrugs3.9570.1364.094
prepareCMapPerturbations5.0370.1164.156
prepareDrugSets 5.536 6.24311.767
prepareENCODEgeneExpression0.0000.0000.001
rankSimilarPerturbations1.9410.0722.013