Nuno Saraiva-Agostinho
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_11 |
| Last Commit: 65ebefa |
| Last Changed Date: 2020-08-30 07:58:15 -0400 (Sun, 30 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:26 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE psichomics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1373/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psichomics 1.14.4 Nuno Saraiva-Agostinho
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | TIMEOUT | skipped | skipped | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: psichomics |
| Version: 1.14.4 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings psichomics_1.14.4.tar.gz |
| StartedAt: 2020-10-17 04:20:50 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:29:32 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 522.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: psichomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings psichomics_1.14.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/psichomics.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.14.4’
* 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 ‘psichomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
queryEnsemblByGene 0.212 0.004 15.283
queryEnsembl 0.081 0.000 6.209
ensemblToUniprot 0.052 0.004 5.066
plotTranscripts 0.024 0.007 5.159
* 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-3.11-bioc/meat/psichomics.Rcheck/00check.log’
for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c psiFastCalc.cpp -o psiFastCalc.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o psiFastCalc.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-psichomics/00new/psichomics/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘colSums’ from package ‘base’ in package ‘psichomics’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (psichomics)
psichomics.Rcheck/tests/spelling.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
0.179 0.015 0.181
psichomics.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(psichomics)
Loading required package: shiny
Loading required package: shinyBS
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
psichomics 1.14.4: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
>
> test_check("psichomics")
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Retrieving rMATS annotation...
Parsing rMATS annotation...
Retrieving rMATS annotation...
Parsing rMATS annotation...
Retrieving MISO annotation...
Parsing MISO annotation...
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Retrieving SUPPA annotation...
Parsing SUPPA annotation...
Retrieving VAST-TOOLS annotation...
Parsing VAST-TOOLS annotation...
ALT3
ALT5
COMBI
EXSK
IR
MERGE3m
MIC
MULTI
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1396 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
30.943 0.748 42.178
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.001 | 0.000 | 0.001 | |
| assignValuePerSubject | 0.018 | 0.000 | 0.034 | |
| blendColours | 0.001 | 0.000 | 0.001 | |
| calculateLoadingsContribution | 0.009 | 0.000 | 0.010 | |
| convertGeneIdentifiers | 0.309 | 0.003 | 0.314 | |
| correlateGEandAS | 0.013 | 0.004 | 0.016 | |
| createGroupByAttribute | 0.001 | 0.000 | 0.001 | |
| createJunctionsTemplate | 0.002 | 0.000 | 0.002 | |
| customRowMeans | 0.001 | 0.000 | 0.012 | |
| diffAnalyses | 0.079 | 0.004 | 0.083 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.052 | 0.004 | 5.066 | |
| filterGeneExpr | 0.009 | 0.000 | 0.009 | |
| filterGroups | 0 | 0 | 0 | |
| filterPSI | 0.02 | 0.00 | 0.02 | |
| getAttributesTime | 0.004 | 0.000 | 0.004 | |
| getDownloadsFolder | 0 | 0 | 0 | |
| getFirebrowseDateFormat | 0 | 0 | 0 | |
| getGeneList | 0.005 | 0.000 | 0.017 | |
| getGtexDataTypes | 0.100 | 0.004 | 0.360 | |
| getGtexTissues | 0.000 | 0.000 | 0.001 | |
| getNumerics | 0.004 | 0.000 | 0.005 | |
| getSampleFromSubject | 0.000 | 0.002 | 0.001 | |
| getSplicingEventFromGenes | 0.004 | 0.001 | 0.006 | |
| getSplicingEventTypes | 0.001 | 0.000 | 0.000 | |
| getSubjectFromSample | 0.000 | 0.000 | 0.001 | |
| getTCGAdataTypes | 0.088 | 0.004 | 0.191 | |
| getValidEvents | 0.006 | 0.000 | 0.005 | |
| groupPerElem | 0.001 | 0.000 | 0.001 | |
| hchart.survfit | 0.343 | 0.019 | 0.512 | |
| isFirebrowseUp | 0.019 | 0.000 | 0.037 | |
| labelBasedOnCutoff | 0.001 | 0.000 | 0.001 | |
| leveneTest | 0.008 | 0.004 | 0.012 | |
| listAllAnnotations | 0.002 | 0.000 | 0.002 | |
| listSplicingAnnotations | 0.004 | 0.000 | 0.004 | |
| loadAnnotation | 0.001 | 0.000 | 0.001 | |
| loadGtexData | 0 | 0 | 0 | |
| loadLocalFiles | 0 | 0 | 0 | |
| loadTCGAdata | 0.015 | 0.002 | 0.040 | |
| missingDataModal | 0 | 0 | 0 | |
| normaliseGeneExpression | 0.034 | 0.000 | 0.034 | |
| optimalSurvivalCutoff | 0.205 | 0.000 | 0.205 | |
| parseCategoricalGroups | 0.001 | 0.000 | 0.001 | |
| parseFirebrowseMetadata | 0.076 | 0.000 | 0.183 | |
| parseMatsEvent | 0.007 | 0.000 | 0.008 | |
| parseMatsGeneric | 0.025 | 0.008 | 0.033 | |
| parseMisoAnnotation | 0.170 | 0.000 | 0.206 | |
| parseMisoEvent | 0.005 | 0.000 | 0.005 | |
| parseMisoEventID | 0.007 | 0.000 | 0.007 | |
| parseMisoGeneric | 0.035 | 0.000 | 0.036 | |
| parseMisoId | 0.001 | 0.000 | 0.001 | |
| parseSplicingEvent | 0.006 | 0.000 | 0.006 | |
| parseSuppaEvent | 0.004 | 0.000 | 0.004 | |
| parseSuppaGeneric | 0.022 | 0.000 | 0.022 | |
| parseTcgaSampleInfo | 0.004 | 0.000 | 0.004 | |
| parseUrlsFromFirebrowseResponse | 0.040 | 0.004 | 0.130 | |
| parseVastToolsEvent | 0.006 | 0.000 | 0.006 | |
| parseVastToolsSE | 0.023 | 0.000 | 0.024 | |
| performICA | 0.011 | 0.000 | 0.010 | |
| performPCA | 0.002 | 0.000 | 0.003 | |
| plot.GEandAScorrelation | 0.392 | 0.000 | 0.392 | |
| plotDistribution | 0.607 | 0.032 | 0.639 | |
| plotGeneExprPerSample | 0.107 | 0.004 | 0.111 | |
| plotGroupIndependence | 0.108 | 0.004 | 0.112 | |
| plotICA | 0.173 | 0.004 | 0.221 | |
| plotLibrarySize | 0.315 | 0.004 | 0.320 | |
| plotPCA | 0.469 | 0.020 | 0.497 | |
| plotPCAvariance | 0.063 | 0.008 | 0.071 | |
| plotProtein | 1.206 | 0.024 | 1.810 | |
| plotRowStats | 1.274 | 0.004 | 1.277 | |
| plotSingleICA | 0.164 | 0.016 | 0.181 | |
| plotSplicingEvent | 1.054 | 0.259 | 1.314 | |
| plotSurvivalCurves | 0.112 | 0.012 | 0.123 | |
| plotSurvivalPvaluesByCutoff | 0.512 | 0.024 | 0.536 | |
| plotTranscripts | 0.024 | 0.007 | 5.159 | |
| prepareAnnotationFromEvents | 0.283 | 0.016 | 0.299 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| prepareJunctionQuantSTAR | 0 | 0 | 0 | |
| prepareSRAmetadata | 0.000 | 0.000 | 0.001 | |
| processSurvTerms | 0.016 | 0.004 | 0.019 | |
| psichomics | 0.001 | 0.000 | 0.001 | |
| quantifySplicing | 0.017 | 0.000 | 0.018 | |
| queryEnsembl | 0.081 | 0.000 | 6.209 | |
| queryEnsemblByGene | 0.212 | 0.004 | 15.283 | |
| queryFirebrowseData | 0.072 | 0.004 | 0.287 | |
| queryPubMed | 0.131 | 0.012 | 0.572 | |
| queryUniprot | 0.165 | 0.004 | 0.643 | |
| readFile | 0.000 | 0.001 | 0.001 | |
| renameDuplicated | 0.000 | 0.001 | 0.001 | |
| renderBoxplot | 0.122 | 0.012 | 0.134 | |
| survdiffTerms | 0.007 | 0.004 | 0.011 | |
| survfit.survTerms | 0.034 | 0.000 | 0.034 | |
| testGroupIndependence | 0.005 | 0.000 | 0.005 | |
| testSurvival | 0.027 | 0.004 | 0.031 | |
| textSuggestions | 0.001 | 0.000 | 0.001 | |
| trimWhitespace | 0.001 | 0.000 | 0.000 | |