Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:18 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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? 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 441/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.15.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/cTRAP
git_branch: master
git_last_commit: 70ef6b8
git_last_commit_date: 2022-04-26 11:51:48 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cTRAP
Version: 1.15.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cTRAP.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings cTRAP_1.15.0.tar.gz
StartedAt: 2022-06-24 00:41:40 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:52:43 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 662.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cTRAP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cTRAP.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings cTRAP_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/cTRAP.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cTRAP/DESCRIPTION' ... OK
* this is package 'cTRAP' version '1.15.0'
* 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  5.0Mb
  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 ... 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                    139.88   2.08  142.00
convertGeneIdentifiers                    24.09   1.72   26.65
plot.referenceComparison                  13.14   0.89   14.04
analyseDrugSetEnrichment                  12.06   1.26   26.78
plot.perturbationChanges                  11.98   0.39   12.37
prepareDrugSets                            6.71   2.72    9.44
filterCMapMetadata                         6.39   0.30    6.97
plotTargetingDrugsVSsimilarPerturbations   5.29   0.50    5.79
downloadENCODEknockdownMetadata            2.00   0.33   11.03
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/cTRAP.Rcheck/00check.log'
for details.



Installation output

cTRAP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/cTRAP_1.15.0.tar.gz && rm -rf cTRAP.buildbin-libdir && mkdir cTRAP.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cTRAP.buildbin-libdir cTRAP_1.15.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL cTRAP_1.15.0.zip && rm cTRAP_1.15.0.tar.gz cTRAP_1.15.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 24 3967k   24  979k    0     0  7265k      0 --:--:-- --:--:-- --:--:-- 7254k
100 3967k  100 3967k    0     0  11.6M      0 --:--:-- --:--:-- --:--:-- 11.6M
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'cTRAP' as cTRAP_1.15.0.zip
* DONE (cTRAP)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'cTRAP' successfully unpacked and MD5 sums checked

Tests output

cTRAP.Rcheck/tests/spelling.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
   0.15    0.06    0.18 

cTRAP.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
  58.53    4.39  213.71 

Example timings

cTRAP.Rcheck/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment12.06 1.2626.78
convertGeneIdentifiers24.09 1.7226.65
downloadENCODEknockdownMetadata 2.00 0.3311.03
filterCMapMetadata6.390.306.97
getCMapConditions000
getCMapPerturbationTypes000
listExpressionDrugSensitivityAssociation000
loadCMapData2.720.152.48
loadCMapZscores2.450.151.97
loadDrugDescriptors0.050.000.04
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation0.860.411.27
parseCMapID000
performDifferentialExpression000
plot.perturbationChanges11.98 0.3912.37
plot.referenceComparison13.14 0.8914.04
plotDrugSetEnrichment139.88 2.08142.00
plotTargetingDrugsVSsimilarPerturbations5.290.505.79
predictTargetingDrugs3.850.534.38
prepareCMapPerturbations3.800.093.44
prepareDrugSets6.712.729.44
prepareENCODEgeneExpression000
rankSimilarPerturbations1.690.001.69