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This page was generated on 2024-03-27 11:37:30 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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

Package 473/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.20.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/cTRAP
git_branch: RELEASE_3_18
git_last_commit: c77177f
git_last_commit_date: 2023-10-24 11:08:57 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for cTRAP on merida1


To the developers/maintainers of the cTRAP package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cTRAP
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-03-26 01:15:39 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 01:34:01 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 1101.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: cTRAP.Rcheck
Warnings: NA

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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/cTRAP.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.20.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .devcontainer
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
Found the following possibly unsafe calls:
File ‘cTRAP/R/shinyInterface_session.R’:
  assignInNamespace("dataTablesFilter", dt_mod, "DT")
* 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                    392.503  2.944 415.767
convertGeneIdentifiers                    29.493  3.012  36.403
plot.referenceComparison                  24.491  1.299  27.212
prepareDrugSets                           11.675 13.732  27.803
analyseDrugSetEnrichment                  21.239  2.509  34.041
plot.perturbationChanges                  22.990  0.749  25.927
filterCMapMetadata                         8.148  1.282  10.960
plotTargetingDrugsVSsimilarPerturbations   8.410  0.788   9.810
predictTargetingDrugs                      6.562  0.583   7.628
prepareCMapPerturbations                   4.841  0.230   5.411
downloadENCODEknockdownMetadata            2.304  0.650  17.355
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  [ FAIL 1 | WARN 2 | SKIP 2 | PASS 243 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On Bioconductor (1): 'test_ENCODE.R:16:5'
  • empty test (1): 'test_drugSetEnrichment.R:88:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plots.R:62:5'): Plot only ranked perturbations ───────────────
  plot$guides$colour not equal to "none".
  target is NULL, current is character
  
  [ FAIL 1 | WARN 2 | SKIP 2 | PASS 243 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
  0.352   0.112   0.442 

cTRAP.Rcheck/tests/testthat.Rout.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 1 | WARN 2 | SKIP 2 | PASS 243 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_ENCODE.R:16:5'
• empty test (1): 'test_drugSetEnrichment.R:88:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plots.R:62:5'): Plot only ranked perturbations ───────────────
plot$guides$colour not equal to "none".
target is NULL, current is character

[ FAIL 1 | WARN 2 | SKIP 2 | PASS 243 ]
Error: Test failures
Execution halted

Example timings

cTRAP.Rcheck/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment21.239 2.50934.041
convertGeneIdentifiers29.493 3.01236.403
downloadENCODEknockdownMetadata 2.304 0.65017.355
filterCMapMetadata 8.148 1.28210.960
getCMapConditions0.0040.0020.005
getCMapPerturbationTypes0.0000.0000.001
listExpressionDrugSensitivityAssociation0.0000.0000.001
loadCMapData4.1750.2734.850
loadCMapZscores3.2570.1703.639
loadDrugDescriptors0.0840.0170.111
loadENCODEsamples0.0010.0010.002
loadExpressionDrugSensitivityAssociation1.3111.6853.440
parseCMapID0.0010.0000.001
performDifferentialExpression0.0030.0010.004
plot.perturbationChanges22.990 0.74925.927
plot.referenceComparison24.491 1.29927.212
plotDrugSetEnrichment392.503 2.944415.767
plotTargetingDrugsVSsimilarPerturbations8.4100.7889.810
predictTargetingDrugs6.5620.5837.628
prepareCMapPerturbations4.8410.2305.411
prepareDrugSets11.67513.73227.803
prepareENCODEgeneExpression0.0010.0000.001
rankSimilarPerturbations1.9830.1122.251