Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:28:54 -0400 (Thu, 12 Apr 2018).
Package 1084/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
psichomics 1.4.5 Nuno Saraiva-Agostinho
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK |
Package: psichomics |
Version: 1.4.5 |
Command: rm -rf psichomics.buildbin-libdir psichomics.Rcheck && mkdir psichomics.buildbin-libdir psichomics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psichomics.buildbin-libdir psichomics_1.4.5.tar.gz >psichomics.Rcheck\00install.out 2>&1 && cp psichomics.Rcheck\00install.out psichomics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=psichomics.buildbin-libdir --install="check:psichomics-install.out" --force-multiarch --no-vignettes --timings psichomics_1.4.5.tar.gz |
StartedAt: 2018-04-12 02:18:48 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 02:26:06 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 437.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: psichomics.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf psichomics.buildbin-libdir psichomics.Rcheck && mkdir psichomics.buildbin-libdir psichomics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psichomics.buildbin-libdir psichomics_1.4.5.tar.gz >psichomics.Rcheck\00install.out 2>&1 && cp psichomics.Rcheck\00install.out psichomics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=psichomics.buildbin-libdir --install="check:psichomics-install.out" --force-multiarch --no-vignettes --timings psichomics_1.4.5.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'psichomics/DESCRIPTION' ... OK * this is package 'psichomics' version '1.4.5' * 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 'psichomics' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOa3qqP/R.INSTALL34e44b54119a/psichomics/man/createEventPlotting.Rd:35: missing file link 'geom_label_repel' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: doc 5.5Mb html 1.2Mb libs 1.5Mb * 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 * loading checks for arch 'i386' ** 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 loading without being on the library search path ... OK * loading checks for arch 'x64' ** 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 loading without being on the library search path ... 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 for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/i386/psichomics.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed ensemblToUniprot 0.27 0.02 10.52 queryEnsemblByGene 0.20 0.03 12.76 queryEnsemblByEvent 0.08 0.00 8.39 plotTranscripts 0.02 0.00 10.02 queryEnsembl 0.02 0.00 12.31 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed ensemblToUniprot 0.17 0 10.50 queryEnsembl 0.05 0 10.90 queryEnsemblByEvent 0.05 0 10.05 queryEnsemblByGene 0.04 0 12.67 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck/00check.log' for details.
psichomics.Rcheck/00install.out
install for i386 * installing *source* package 'psichomics' ... ** libs C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -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:59:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t col=0; col < mat.ncol(); col++) { ^ psiFastCalc.cpp:60:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t idx=0; idx < inc.length(); idx++) { ^ psiFastCalc.cpp:63:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t k=0; k < incIdx.length(); k++) ^ psiFastCalc.cpp:68:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t k=0; k < excIdx.length(); k++) ^ C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o psiFastCalc.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/i386 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'psichomics' finding HTML links ... done ASquantFileInput html addTCGAdata html appServer html appUI html appendNewGroups html areSplicingEvents html articleUI html assignColours html basicStats html blendColours html browserHistory html bsModal2 html calculateInclusionLevels html calculateLoadingsContribution html checkFileFormat html checkFirebrowse html checkIntegrity html checkSurvivalInput html closeProgress html clusterICAset html clusterSet html correlateGEandAS html createDataTab html createDensitySparklines html createEventPlotting html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOa3qqP/R.INSTALL34e44b54119a/psichomics/man/createEventPlotting.Rd:35: missing file link 'geom_label_repel' createGroup html createGroupByAttribute html createGroupById html createGroupFromInput html createJunctionsTemplate html createOptimalSurvData html createSparklines html diffAnalyses html diffAnalysesPlotSet html diffAnalysesSet html diffAnalysesTableSet html diffExpressionPlotSet html diffExpressionSet html diffExpressionTableSet html disableTab html display html downloadFiles html endProcess html ensemblToUniprot html escape html eventPlotOptions html export_highcharts html fileBrowser html fileBrowserInput html filterGroups html fisher html fligner html geNormalisationFilteringInterface html geneExprFileInput html geneExprSurvSet html getASevent html getASevents html getAttributesTime html getClinicalDataForSurvival html getClinicalMatchFrom html getData html getDataRows html getDifferentialAnalyses html getDifferentialExpression html getDownloadsFolder html getEvent html getFirebrowseCohorts html getFirebrowseDataTypes html getFirebrowseDateFormat html getFirebrowseDates html getGenes html getGenesFromSplicingEvents html getGlobal html getGroups html getGtexTissues html getHidden html getHighlightedPoints html getMatchingSamples html getNumerics html getPatientFromSample html getServerFunctions html getSplicingEventCoordinates html getSplicingEventFromGenes html getSplicingEventTypes html getUiFunctions html getValidEvents html getValuePerPatient html ggplotServer html ggplotTooltip html ggplotUI html globalSelectize html groupByAttribute html groupByExpression html groupByGrep html groupById html groupManipulation html groupManipulationInput html groupPerElem html groupsServerOnce html hc_scatter html hchart.survfit html inclusionLevelsInterface html inlineDialog html insideFile html is.whole html isFirebrowseUp html joinEventsPerType html junctionString html kruskal html labelBasedOnCutoff html levene html leveneTest html linkToArticle html linkToRunJS html listAllAnnotations html listSplicingAnnotations html loadAnnotation html loadBy html loadCustomSplicingAnnotationSet html loadFile html loadFileFormats html loadFirebrowseData html loadFirebrowseFolders html loadGeneExpressionSet html loadGtexData html loadGtexDataShiny html loadGtexFile html loadLocalFiles html loadSplicingQuantificationSet html loadTCGAsampleMetadata html loadedDataModal html matchSplicingEventsWithGenes html missingDataModal html modTabPanel html navSelectize html noinfo html normaliseGeneExpression html operateOnGroups html optimSurvDiffSet html optimalSurvivalCutoff html parseCategoricalGroups html parseDateResponse html parseFirebrowseMetadata html parseMatsEvent html parseMatsGeneric html parseMisoAnnotation html parseMisoEvent html parseMisoEventID html parseMisoGeneric html parseMisoId html parseSampleGroups html parseSplicingEvent html parseSuppaEvent html parseSuppaGeneric html parseTcgaSampleInfo html parseUniprotXML html parseUrlsFromFirebrowseResponse html parseValidFile html parseVastToolsEvent html parseVastToolsSE html patientMultiMatchWarning html performICA html performPCA html plotClusters html plotCorrelation html plotDistribution html plotGroupIndependence html plotICA html plotPCA html plotPointsStyle html plotProtein html plotSingleICA html plotSurvivalCurves html plotTranscripts html plotVariance html plottableXranges html prepareAnnotationFromEvents html prepareEventPlotOptions html prepareFileBrowser html prepareFirebrowseArchives html processButton html finding level-2 HTML links ... done processDatasetNames html processSurvData html processSurvTerms html processSurvival html psichomics html pubmedUI html quantifySplicing html quantifySplicingSet html queryEnsembl html queryEnsemblByEvent html queryEnsemblByGene html queryFirebrowseData html queryPubMed html queryUniprot html readAnnot html readFile html reduceDimensionality html renameDuplicated html renameGroups html renderDataTableSparklines html renderGeneticInfo html renderGroupInterface html renderProteinInfo html rm.null html roundDigits html roundMinDown html rowMeans html rowVars html selectGroupsUI html selectizeGeneInput html setFirebrowseData html setLocalData html setOperation html setOperationIcon html showAlert html showGroupsTable html sidebar html signifDigits html singleDiffAnalyses html sortCoordinates html spearman html startProcess html startProgress html styleModal html survdiff.survTerms html survfit.survTerms html tabDataset html table2html html tableRow html testGroupIndependence html testSingleIndependence html testSurvival html testSurvivalCutoff html textSuggestions html toJSarray html transformData html transformOptions html transformValues html trimWhitespace html ttest html uniqueBy html updateClinicalParams html updateFileBrowserInput html updateProgress html vennEvents html wilcox html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'psichomics' ... ** libs C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -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:59:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t col=0; col < mat.ncol(); col++) { ^ psiFastCalc.cpp:60:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t idx=0; idx < inc.length(); idx++) { ^ psiFastCalc.cpp:63:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t k=0; k < incIdx.length(); k++) ^ psiFastCalc.cpp:68:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (size_t k=0; k < excIdx.length(); k++) ^ C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o psiFastCalc.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'psichomics' as psichomics_1.4.5.zip * DONE (psichomics) In R CMD INSTALL In R CMD INSTALL
psichomics.Rcheck/tests_i386/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 Start the visual interface by running the function psichomics() Attaching package: 'psichomics' The following object is masked from 'package:base': rowMeans > > test_check("psichomics") | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% 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... | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% 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: 1071 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 11.85 0.35 24.89 |
psichomics.Rcheck/tests_x64/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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(psichomics) Loading required package: shiny Loading required package: shinyBS Start the visual interface by running the function psichomics() Attaching package: 'psichomics' The following object is masked from 'package:base': rowMeans > > test_check("psichomics") | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% 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... | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% 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: 1055 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 13.54 0.29 24.98 |
psichomics.Rcheck/examples_i386/psichomics-Ex.timings
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psichomics.Rcheck/examples_x64/psichomics-Ex.timings
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