Nuno Saraiva-Agostinho
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_9 |
| Last Commit: e63d018 |
| Last Changed Date: 2019-10-07 13:21:54 -0400 (Mon, 07 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:09:50 -0400 (Wed, 16 Oct 2019).
| Package 1272/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psichomics 1.10.2 Nuno Saraiva-Agostinho
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: psichomics |
| Version: 1.10.2 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings psichomics_1.10.2.tar.gz |
| StartedAt: 2019-10-16 04:08:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:14:27 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 376.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: psichomics.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings psichomics_1.10.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/psichomics.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.10.2’ * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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-3.9-bioc/meat/psichomics.Rcheck/00check.log’ for details.
psichomics.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c psiFastCalc.cpp -o psiFastCalc.o
psiFastCalc.cpp: In function ‘Rcpp::NumericMatrix psiFastCalc(const NumericMatrix&, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)’:
psiFastCalc.cpp:30:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
~~~~^~~~~~~~~~~~
psiFastCalc.cpp:31:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t idx=0; idx < incA.length(); idx++) {
~~~~^~~~~~~~~~~~~~~
psiFastCalc.cpp: In function ‘Rcpp::NumericMatrix psiFastCalc2(const NumericMatrix&, const List&, const List&, int)’:
psiFastCalc.cpp:62:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
~~~~^~~~~~~~~~~~
psiFastCalc.cpp:63:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t idx=0; idx < inc.length(); idx++) {
~~~~^~~~~~~~~~~~~~
psiFastCalc.cpp:66:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t k=0; k < incIdx.length(); k++)
~~^~~~~~~~~~~~~~~~~
psiFastCalc.cpp:71:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t k=0; k < excIdx.length(); k++)
~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o psiFastCalc.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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
** 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/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
Start the visual interface by running the function psichomics()
Attaching package: 'psichomics'
The following object is masked from 'package:base':
rowMeans
>
> test_check("psichomics")
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Retrieving protein annotation from UniProt...
Plotting protein domains...
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
IR
MERGE3m
MIC
EXSK
MULTI
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1078 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
22.753 0.797 29.613
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.000 | 0.000 | 0.001 | |
| blendColours | 0.001 | 0.000 | 0.001 | |
| calculateLoadingsContribution | 0.853 | 0.004 | 0.857 | |
| convertGeneIdentifiers | 0.413 | 0.000 | 0.287 | |
| correlateGEandAS | 0.022 | 0.000 | 0.082 | |
| createGroupByAttribute | 0.001 | 0.001 | 0.002 | |
| createJunctionsTemplate | 0.001 | 0.002 | 0.003 | |
| diffAnalyses | 0.108 | 0.004 | 0.112 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.323 | 0.000 | 0.947 | |
| filterGeneExpr | 0.017 | 0.000 | 0.017 | |
| filterGroups | 0.001 | 0.000 | 0.000 | |
| filterPSI | 0.017 | 0.000 | 0.017 | |
| getAttributesTime | 0.004 | 0.000 | 0.005 | |
| getDownloadsFolder | 0.001 | 0.000 | 0.000 | |
| getFirebrowseDataTypes | 0.001 | 0.000 | 0.001 | |
| getFirebrowseDateFormat | 0.001 | 0.000 | 0.000 | |
| getFirebrowseDates | 0.096 | 0.000 | 0.190 | |
| getGeneList | 0.008 | 0.003 | 0.031 | |
| getMatchingSamples | 0.000 | 0.002 | 0.001 | |
| getNumerics | 0.002 | 0.001 | 0.003 | |
| getPatientFromSample | 0.000 | 0.000 | 0.001 | |
| getSplicingEventFromGenes | 0.003 | 0.000 | 0.003 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getValidEvents | 0.004 | 0.000 | 0.004 | |
| getValuePerPatient | 0.006 | 0.000 | 0.007 | |
| groupPerElem | 0.001 | 0.000 | 0.001 | |
| hchart.survfit | 0.317 | 0.037 | 0.499 | |
| isFirebrowseUp | 0.006 | 0.000 | 0.024 | |
| labelBasedOnCutoff | 0 | 0 | 0 | |
| leveneTest | 0.008 | 0.000 | 0.008 | |
| listAllAnnotations | 0 | 0 | 0 | |
| listSplicingAnnotations | 0 | 0 | 0 | |
| loadAnnotation | 0 | 0 | 0 | |
| loadFirebrowseData | 0 | 0 | 0 | |
| loadLocalFiles | 0.001 | 0.000 | 0.000 | |
| missingDataModal | 0 | 0 | 0 | |
| normaliseGeneExpression | 0.02 | 0.00 | 0.02 | |
| optimalSurvivalCutoff | 0.135 | 0.000 | 0.135 | |
| parseCategoricalGroups | 0.001 | 0.000 | 0.001 | |
| parseFirebrowseMetadata | 0.068 | 0.007 | 0.177 | |
| parseMatsEvent | 0.009 | 0.000 | 0.009 | |
| parseMatsGeneric | 0.033 | 0.004 | 0.038 | |
| parseMisoAnnotation | 0.283 | 0.068 | 0.406 | |
| parseMisoEvent | 0.005 | 0.000 | 0.005 | |
| parseMisoEventID | 0.006 | 0.000 | 0.006 | |
| parseMisoGeneric | 0.034 | 0.004 | 0.038 | |
| parseMisoId | 0 | 0 | 0 | |
| parseSampleGroups | 0.001 | 0.000 | 0.002 | |
| parseSplicingEvent | 0.003 | 0.000 | 0.003 | |
| parseSuppaEvent | 0.004 | 0.000 | 0.004 | |
| parseSuppaGeneric | 0.022 | 0.000 | 0.022 | |
| parseTcgaSampleInfo | 0.003 | 0.000 | 0.003 | |
| parseUrlsFromFirebrowseResponse | 0.032 | 0.001 | 0.096 | |
| parseVastToolsEvent | 0.007 | 0.000 | 0.007 | |
| parseVastToolsSE | 0.020 | 0.004 | 0.024 | |
| performICA | 0.044 | 0.004 | 0.048 | |
| performPCA | 0.002 | 0.000 | 0.002 | |
| plot.GEandAScorrelation | 0.487 | 0.004 | 0.491 | |
| plotDistribution | 0.056 | 0.004 | 0.060 | |
| plotGeneExprPerSample | 0.165 | 0.012 | 0.178 | |
| plotGroupIndependence | 0.228 | 0.000 | 0.236 | |
| plotICA | 0.117 | 0.000 | 0.382 | |
| plotPCA | 0.206 | 0.012 | 0.217 | |
| plotProtein | 1.080 | 0.067 | 2.998 | |
| plotRowStats | 1.014 | 0.000 | 1.013 | |
| plotSingleICA | 0.268 | 0.032 | 0.301 | |
| plotSurvivalCurves | 0.110 | 0.016 | 0.126 | |
| plotTranscripts | 0.031 | 0.000 | 1.021 | |
| plotVariance | 0.05 | 0.02 | 0.07 | |
| prepareAnnotationFromEvents | 0.272 | 0.000 | 0.273 | |
| prepareFirebrowseArchives | 0.001 | 0.000 | 0.000 | |
| prepareJunctionQuantSTAR | 0 | 0 | 0 | |
| prepareSRAmetadata | 0 | 0 | 0 | |
| processSurvTerms | 0.004 | 0.000 | 0.004 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.004 | 0.004 | 0.007 | |
| queryEnsembl | 0.049 | 0.001 | 0.849 | |
| queryEnsemblByGene | 0.176 | 0.003 | 4.009 | |
| queryFirebrowseData | 0.045 | 0.000 | 0.172 | |
| queryPubMed | 0.121 | 0.020 | 0.513 | |
| queryUniprot | 0.089 | 0.000 | 1.408 | |
| readFile | 0.002 | 0.000 | 0.001 | |
| renameDuplicated | 0.001 | 0.000 | 0.001 | |
| renderBoxplot | 0.126 | 0.004 | 0.130 | |
| rowMeans | 0.001 | 0.000 | 0.000 | |
| sidebar | 0.012 | 0.000 | 0.012 | |
| survdiffTerms | 0.009 | 0.000 | 0.009 | |
| survfit.survTerms | 0.029 | 0.000 | 0.028 | |
| testGroupIndependence | 0.005 | 0.000 | 0.004 | |
| testSurvival | 0.026 | 0.000 | 0.027 | |
| textSuggestions | 0.000 | 0.000 | 0.001 | |
| trimWhitespace | 0 | 0 | 0 | |