Nuno Saraiva-Agostinho
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_8 |
| Last Commit: 5490eef |
| Last Changed Date: 2019-03-27 10:18:03 -0400 (Wed, 27 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:13 -0400 (Sat, 13 Apr 2019).
| Package 1211/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psichomics 1.8.2 Nuno Saraiva-Agostinho
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: psichomics |
| Version: 1.8.2 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings psichomics_1.8.2.tar.gz |
| StartedAt: 2019-04-13 04:43:52 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:52:52 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 540.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: psichomics.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings psichomics_1.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/psichomics.Rcheck' * using R version 3.5.3 (2019-03-11) * 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 '1.8.2' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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-3.8-bioc/tmpdir/Rtmps90wYD/R.INSTALL1db8166535c7/psichomics/man/createEventPlotting.Rd:36: file link 'geom_label_repel' in package 'ggrepel' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/psichomics.Rcheck/00install.out' for details. * 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 * 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 * 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 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-3.8-bioc/R/library/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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/psichomics.Rcheck/00check.log' for details.
psichomics.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/psichomics_1.8.2.tar.gz && rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.8.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL psichomics_1.8.2.zip && rm psichomics_1.8.2.tar.gz psichomics_1.8.2.zip
###
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install for i386
* installing *source* package 'psichomics' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/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: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++)
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o psiFastCalc.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/i386
** 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
converting help for package 'psichomics'
finding HTML links ... done
ASquantFileInput html
addObjectAttrs html
addTCGAdata html
analysesTableSet 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
clusterICAset html
clusterSet html
colSums-EList-method html
finding level-2 HTML links ... done
colourInputMod html
convertGeneIdentifiers html
correlateGEandAS html
createDataTab html
createDensitySparklines html
createEventPlotting html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmps90wYD/R.INSTALL1db8166535c7/psichomics/man/createEventPlotting.Rd:36: file link 'geom_label_repel' in package 'ggrepel' does not exist and so has been treated as a topic
createGroup html
createGroupByAttribute html
createGroupById html
createGroupFromInput html
createJunctionsTemplate html
createOptimalSurvData html
createSparklines html
diffAnalyses html
diffExpressionSet html
diffSplicingSet html
disableTab html
discardOutsideSamplesFromGroups html
display html
downloadFiles html
ensemblToUniprot html
escape html
eventPlotOptions html
export_highcharts html
fileBrowser html
fileBrowserInput html
filterGeneExpr html
filterGroups html
filterPSI html
findASeventsFromGene html
geNormalisationFilteringInterface html
geneExprFileInput html
geneExprSurvSet html
getASevent html
getASevents html
getAttributesTime html
getClinicalDataForSurvival html
getClinicalMatchFrom html
getData html
getDataRows html
getDifferentialExpression html
getDifferentialSplicing html
getDownloadsFolder html
getFirebrowseDataTypes html
getFirebrowseDateFormat html
getFirebrowseDates html
getGeneList html
getGlobal html
getGroups html
getGtexDataTypes 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
groupManipulation html
groupManipulationInput html
groupPerElem html
groupsServerOnce html
hc_scatter html
hchart.survfit html
inclusionLevelsInterface html
inlineDialog html
insideFile html
is.whole html
isFile html
isFirebrowseUp html
isRStudioServer html
joinEventsPerType html
junctionString html
labelBasedOnCutoff 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
loadSRAproject html
loadSplicingQuantificationSet html
loadTCGAsampleMetadata html
loadedDataModal html
matchGroupASeventsAndGenes html
matchGroupPatientsAndSamples 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
plot.GEandAScorrelation html
plotClusters html
plotDistribution html
plotGeneExprPerSample html
plotGroupIndependence html
plotICA html
plotPCA html
plotPointsStyle html
plotProtein html
plotRowStats html
plotSingleICA html
plotSurvivalCurves html
plotSurvivalPvaluesByCutoff html
plotTranscripts html
plotVariance html
plottableXranges html
prepareAnnotationFromEvents html
prepareEventPlotOptions html
prepareFileBrowser html
prepareFirebrowseArchives html
prepareJunctionQuantSTAR html
preparePreMadeGroupForSelection html
prepareSRAmetadata html
prepareWordBreak html
print.geneList html
processAndSaveSRAdata html
processButton html
processDatasetNames html
processSurvData html
processSurvTerms html
processSurvival html
psichomics html
pubmedUI html
quantifySplicing html
quantifySplicingSet html
queryEnsembl html
queryEnsemblByGene html
queryFirebrowseData html
queryPubMed html
queryUniprot html
readAnnot html
readFile html
reduceDimensionality html
renameDuplicated html
renameGroups html
renderBoxplot html
renderDataTableSparklines html
renderGeneticInfo html
renderGroupInterface html
renderProteinInfo html
rm.null html
roundDigits html
roundMinDown html
rowMeans html
selectGroupsUI html
selectPreMadeGroup html
selectizeGeneInput html
setFirebrowseData html
setLocalData html
setOperation html
setOperationIcon html
showAlert html
showGroupsTable html
sidebar html
signifDigits html
singleDiffAnalyses html
sortCoordinates html
startProcess html
startProgress html
styleModal html
sub-.GEandAScorrelation html
subsetGeneExpressionFromMatchingGenes 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
uniqueBy html
updateClinicalParams html
updateFileBrowserInput 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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/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: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++)
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o psiFastCalc.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psichomics' as psichomics_1.8.2.zip
* DONE (psichomics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'psichomics' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
psichomics.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
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: 1090 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
21.57 2.15 33.85
|
psichomics.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
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: 1090 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
20.46 0.85 31.21
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psichomics.Rcheck/examples_i386/psichomics-Ex.timings
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psichomics.Rcheck/examples_x64/psichomics-Ex.timings
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