Nuno Saraiva-Agostinho
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 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 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:17 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 435/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cTRAP 1.13.0 (landing page) Nuno Saraiva-Agostinho
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: cTRAP |
| Version: 1.13.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cTRAP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cTRAP_1.13.0.tar.gz |
| StartedAt: 2022-03-17 18:50:45 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:02:04 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 678.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cTRAP.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cTRAP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cTRAP_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cTRAP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'cTRAP' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
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 ... WARNING
Warning in file 'R/shinyInterface.R':
unable to translate 'For data with <U+2265> 2 cell lines' to native encoding
* 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 120.56 1.11 124.91
convertGeneIdentifiers 20.35 1.84 25.28
filterCMapMetadata 5.87 9.49 17.95
loadCMapData 3.92 9.98 14.91
plot.perturbationChanges 12.84 0.89 13.73
plot.referenceComparison 11.55 1.77 13.31
analyseDrugSetEnrichment 9.19 1.81 42.08
prepareDrugSets 4.80 2.04 6.83
downloadENCODEknockdownMetadata 1.74 0.45 28.66
* 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 WARNING, 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/cTRAP.Rcheck/00check.log'
for details.
cTRAP.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cTRAP
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'cTRAP'
finding HTML links ... done
ENCODEmetadata html
GCT-class html
HTMLfast html
analyseDrugSetEnrichment html
as.table.referenceComparison html
cTRAP html
calculateCellLineMean html
calculateEvenlyDistributedBins html
checkColnames html
chunkColumns html
closeOpenHandles html
cmapMetadata html
cmapPerturbationsCompounds html
cmapPerturbationsKD html
compareQuantile html
compareWithAllMethods html
convertENSEMBLtoGeneSymbols html
convertGeneIdentifiers html
counts html
diffExprStat html
dimnames.expressionDrugSensitivityAssociation
html
dot-plotBubbles html
dot-prepareNavPage html
dot-traceInList html
downloadENCODEknockdownMetadata html
downloadIfNotFound html
filterCMapMetadata html
findIntersectingCompounds html
fix.datatypes html
getCMapConditions html
getCMapPerturbationTypes html
getENCODEcontrols html
launchCMapDataLoader html
launchDiffExprLoader html
launchDrugSetEnrichmentAnalyser html
launchMetadataViewer html
launchResultPlotter html
listExpressionDrugSensitivityAssociation
html
loadCMapData html
loadCMapZscores html
loadCTRPgeneExpression html
loadDrugDescriptors html
loadENCODEsample html
loadENCODEsamples html
loadExpressionDrugSensitivityAssociation
html
loadNCI60drugSensitivity html
matchStatsWithDrugSetsID html
parseCMapID html
performDifferentialExpression html
performGSEA html
plot.perturbationChanges html
plot.referenceComparison html
plotDrugSetEnrichment html
plotESplot html
plotGSEA html
plotMetricDistribution html
plotSingleCorr html
plotTargetingDrugsVSsimilarPerturbations
html
predictTargetingDrugs html
prepareCMapPerturbations html
prepareDrugSets html
prepareENCODEgeneExpression html
prepareExpressionDrugSensitivityAssociation
html
prepareGSEAgenesets html
prepareSetsCompoundInfo html
prepareStatsCompoundInfo html
prepareWordBreak html
print.similarPerturbations html
processByChunks html
processIds html
rankAgainstReference html
rankColumns html
rankSimilarPerturbations html
readGctxIds html
readGctxMeta html
stripStr html
subsetData html
subsetDim html
subsetToIds html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'ppiStats' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'VariantExperiment' is missing or broken
done
cTRAP.Rcheck/tests/spelling.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
0.14 0.07 0.20
cTRAP.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
49.70 5.95 201.84
cTRAP.Rcheck/cTRAP-Ex.timings
| name | user | system | elapsed | |
| analyseDrugSetEnrichment | 9.19 | 1.81 | 42.08 | |
| convertGeneIdentifiers | 20.35 | 1.84 | 25.28 | |
| downloadENCODEknockdownMetadata | 1.74 | 0.45 | 28.66 | |
| filterCMapMetadata | 5.87 | 9.49 | 17.95 | |
| getCMapConditions | 0 | 0 | 0 | |
| getCMapPerturbationTypes | 0 | 0 | 0 | |
| listExpressionDrugSensitivityAssociation | 0 | 0 | 0 | |
| loadCMapData | 3.92 | 9.98 | 14.91 | |
| loadCMapZscores | 2.55 | 0.41 | 2.54 | |
| loadDrugDescriptors | 0.02 | 0.03 | 0.05 | |
| loadENCODEsamples | 0 | 0 | 0 | |
| loadExpressionDrugSensitivityAssociation | 0.70 | 0.31 | 1.02 | |
| parseCMapID | 0 | 0 | 0 | |
| performDifferentialExpression | 0 | 0 | 0 | |
| plot.perturbationChanges | 12.84 | 0.89 | 13.73 | |
| plot.referenceComparison | 11.55 | 1.77 | 13.31 | |
| plotDrugSetEnrichment | 120.56 | 1.11 | 124.91 | |
| plotTargetingDrugsVSsimilarPerturbations | 3.83 | 0.98 | 4.81 | |
| predictTargetingDrugs | 3.05 | 0.89 | 3.94 | |
| prepareCMapPerturbations | 3.67 | 0.31 | 3.47 | |
| prepareDrugSets | 4.80 | 2.04 | 6.83 | |
| prepareENCODEgeneExpression | 0 | 0 | 0 | |
| rankSimilarPerturbations | 1.28 | 0.03 | 1.31 | |