Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 474/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.24.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/cTRAP
git_branch: RELEASE_3_20
git_last_commit: 738ffa4
git_last_commit_date: 2024-10-29 10:32:37 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped


CHECK results for cTRAP on lconway

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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2024-11-19 21:02:42 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 21:16:26 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 824.0 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cTRAP.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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")

plotComparison: no visible binding for global variable ‘.data’
plotMetricDistribution: no visible binding for global variable ‘.data’
plotSingleCorr: no visible binding for global variable ‘.data’
plotTargetingDrug: no visible binding for global variable ‘.data’
plotTargetingDrugsVSsimilarPerturbations: no visible binding for global
  variable ‘.data’
Undefined global functions or variables:
  .data
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'compareWithAllMethods.Rd':
  ‘rankByAscending’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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                    140.301  1.876 142.661
convertGeneIdentifiers                    15.021  1.691  24.846
plot.referenceComparison                  14.180  1.300  15.532
analyseDrugSetEnrichment                  11.732  1.818  61.318
plot.perturbationChanges                   9.845  0.544  10.417
prepareDrugSets                            4.149  3.463   7.645
plotTargetingDrugsVSsimilarPerturbations   4.619  1.023   5.678
filterCMapMetadata                         4.732  0.561  13.033
downloadENCODEknockdownMetadata            2.172  0.613  59.759
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  0.164   0.065   0.225 

cTRAP.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 243 ]

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

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
 48.256   6.173  85.419 

Example timings

cTRAP.Rcheck/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment11.732 1.81861.318
convertGeneIdentifiers15.021 1.69124.846
downloadENCODEknockdownMetadata 2.172 0.61359.759
filterCMapMetadata 4.732 0.56113.033
getCMapConditions0.0020.0010.002
getCMapPerturbationTypes0.0000.0010.001
listExpressionDrugSensitivityAssociation000
loadCMapData2.2710.1872.698
loadCMapZscores1.7150.1651.895
loadDrugDescriptors0.0360.0100.048
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation0.5430.4571.042
parseCMapID0.0000.0000.001
performDifferentialExpression0.0010.0000.001
plot.perturbationChanges 9.845 0.54410.417
plot.referenceComparison14.180 1.30015.532
plotDrugSetEnrichment140.301 1.876142.661
plotTargetingDrugsVSsimilarPerturbations4.6191.0235.678
predictTargetingDrugs3.2540.9654.273
prepareCMapPerturbations3.9050.2684.216
prepareDrugSets4.1493.4637.645
prepareENCODEgeneExpression000
rankSimilarPerturbations1.4390.1781.627