Nuno Saraiva-Agostinho
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_7 |
| Last Commit: 670cb8a |
| Last Changed Date: 2018-10-02 05:35:55 -0400 (Tue, 02 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:43:02 -0400 (Wed, 17 Oct 2018).
| Package 1145/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psichomics 1.6.2 Nuno Saraiva-Agostinho
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: psichomics |
| Version: 1.6.2 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/psichomics_1.6.2.tar.gz && rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL psichomics_1.6.2.zip && rm psichomics_1.6.2.tar.gz psichomics_1.6.2.zip |
| StartedAt: 2018-10-16 20:37:46 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:41:32 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 226.4 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/psichomics_1.6.2.tar.gz && rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL psichomics_1.6.2.zip && rm psichomics_1.6.2.tar.gz psichomics_1.6.2.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
100 4475k 100 4475k 0 0 43.5M 0 --:--:-- --:--:-- --:--:-- 46.4M
install for i386
* installing *source* package 'psichomics' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
** help
*** installing help indices
converting help for package 'psichomics'
finding HTML links ... done
ASquantFileInput html
addObjectAttrs html
addTCGAdata html
analysesPlotSet 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
closeProgress html
clusterICAset html
clusterSet html
colourInputMod html
correlateGEandAS html
createDataTab html
createDensitySparklines html
createEventPlotting html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpSUnGhF/R.INSTALL249412a75ca5/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
display html
downloadFiles html
endProcess html
ensemblToUniprot html
escape html
eventPlotOptions html
export_highcharts html
fileBrowser html
fileBrowserInput html
filterGroups html
findASeventsFromGene 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
getDifferentialExpression html
getDifferentialSplicing 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
isFile html
isFirebrowseUp html
isRStudioServer 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
loadSRAproject html
loadSplicingQuantificationSet html
loadTCGAsampleMetadata html
loadedDataModal 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
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
prepareSRAmetadata html
prepareWordBreak 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
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
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
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
* MD5 sums
packaged installation of 'psichomics' as psichomics_1.6.2.zip
* DONE (psichomics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'psichomics' successfully unpacked and MD5 sums checked
In R CMD INSTALL