Nuno Saraiva-Agostinho
| Snapshot Date: 2020-08-11 14:50:18 -0400 (Tue, 11 Aug 2020) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_11 |
| Last Commit: 65bf22b |
| Last Changed Date: 2020-06-16 05:46:59 -0400 (Tue, 16 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-08-12 12:45:37 -0400 (Wed, 12 Aug 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 1.14.1 Nuno Saraiva-Agostinho
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: psichomics |
| Version: 1.14.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings psichomics_1.14.1.tar.gz |
| StartedAt: 2020-08-12 06:02:55 -0400 (Wed, 12 Aug 2020) |
| EndedAt: 2020-08-12 06:14:30 -0400 (Wed, 12 Aug 2020) |
| EllapsedTime: 695.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: psichomics.Rcheck |
| Warnings: 4 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings psichomics_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/psichomics.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.14.1'
* 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-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plot.GEandAScorrelation.Rd:71: file link 'loess.smooth' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plotDistribution.Rd:34: file link 'density.default' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plotDistribution.Rd:41: file link 'bw.nrd' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plotDistribution.Rd:89: file link 'approx' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/processButton.Rd:19: file link 'validateCssUnit' in package 'shiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/reduceDimensionality.Rd:25: file link 'as.numeric' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/reduceDimensionality.Rd:26: file link 'is.numeric' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/renderDataTableSparklines.Rd:22: file link 'dataTableOutput' in package 'shiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/styleModal.Rd:41: file link 'removeModal' in package 'shiny' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/psichomics.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
R 1.3Mb
html 1.2Mb
libs 2.0Mb
* 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 ... WARNING
Warnings in file 'R/analysis.R':
unable to translate '<U+2206> Variance' to native encoding
unable to translate '<U+2206> Median' to native encoding
* 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-3.11-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)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/psichomics/libs/x64/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' ... WARNING
Found the following significant warnings:
Warning: 'hcboxplot' is deprecated.
Warning: 'hcboxplot' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: 'hcboxplot' is deprecated.
Warning: 'hcboxplot' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotPCA 0.34 0.17 17.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'spelling.R'
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 4 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-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://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/psichomics_1.14.1.tar.gz && rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL psichomics_1.14.1.zip && rm psichomics_1.14.1.tar.gz psichomics_1.14.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
18 3783k 18 704k 0 0 10.8M 0 --:--:-- --:--:-- --:--:-- 12.0M
100 3783k 100 3783k 0 0 38.9M 0 --:--:-- --:--:-- --:--:-- 41.5M
install for i386
* installing *source* package 'psichomics' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
~~~~^~~~~~~~~~~~
psiFastCalc.cpp:31:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-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 of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
~~~~^~~~~~~~~~~~
psiFastCalc.cpp:63:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (size_t idx=0; idx < inc.length(); idx++) {
~~~~^~~~~~~~~~~~~~
psiFastCalc.cpp:66:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (size_t k=0; k < incIdx.length(); k++)
~~^~~~~~~~~~~~~~~~~
psiFastCalc.cpp:71:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (size_t k=0; k < excIdx.length(); k++)
~~^~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/psichomics.buildbin-libdir/00LOCK-psichomics/00new/psichomics/libs/i386
** R
Warning in parse(outFile) :
unable to translate '<U+2206> Variance' to native encoding
Warning in parse(outFile) :
unable to translate '<U+2206> Median' to native encoding
** inst
** byte-compile and prepare package for lazy loading
Warning in parse(n = -1, file = file, srcfile = NULL, keep.source = FALSE) :
unable to translate '<U+2206> Variance' to native encoding
Warning in parse(n = -1, file = file, srcfile = NULL, keep.source = FALSE) :
unable to translate '<U+2206> Median' to native encoding
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
assignValuePerSubject html
basicStats html
blendColours html
browserHistory html
bsModal2 html
calculateInclusionLevels html
calculateLoadingsContribution html
checkFileFormat html
checkFirebrowse html
checkGroupType 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
createGroup html
createGroupByAttribute html
createGroupById html
createGroupFromInput html
createJunctionsTemplate html
createOptimalSurvData html
createSparklines html
diagramSplicingEvent html
diffAnalyses html
diffExpressionSet html
diffSplicingSet html
disableTab html
discardOutsideSamplesFromGroups html
display html
downloadFiles html
ensemblToUniprot html
escape html
eventPlotOptions html
exportGroupsToFile html
export_highcharts html
fileBrowser html
fileBrowserInput html
filterGeneExpr html
filterGroups html
filterPSI html
findASeventsFromGene html
geNormalisationFilteringInterface html
geneExprFileInput html
geneExprSurvSet html
getAttributesTime html
getClinicalDataForSurvival html
getClinicalMatchFrom html
getData html
getDataRows html
getDifferentialExpression html
getDifferentialSplicing html
getDownloadsFolder html
getFirebrowseDateFormat html
getGeneList html
getGlobal html
getGroups html
getGtexDataTypes html
getGtexTissues html
getHidden html
getHighlightedPoints html
getMatchingSamples html
getNumerics html
getServerFunctions html
getSplicingEventCoordinates html
getSplicingEventFromGenes html
getSplicingEventTypes html
getSubjectFromSample html
getTCGAdataTypes html
getUiFunctions html
getValidEvents 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
importGroupsFrom html
inclusionLevelsInterface html
inlineDialog html
insideFile html
is.whole html
isFile html
isFirebrowseUp html
isRStudioServer html
joinEventsPerType html
junctionString html
labelBasedOnCutoff html
leveneTest html
linkToArticles html
linkToRunJS html
listAllAnnotations html
listSplicingAnnotations html
loadAnnotation html
loadBy html
loadCustomSplicingAnnotationSet html
loadFile html
loadFileFormats html
loadFirebrowseFolders html
loadGeneExpressionSet html
loadGtexData html
loadGtexDataShiny html
loadGtexFile html
loadLocalFiles html
loadSRAproject html
loadSplicingQuantificationSet html
loadTCGAdata html
loadTCGAsampleMetadata html
loadedDataModal html
matchGroupASeventsAndGenes html
matchGroupSubjectsAndSamples html
matchSplicingEventsWithGenes html
missingDataModal html
modTabPanel html
navSelectize html
normaliseGeneExpression html
operateOnGroups html
optimSurvDiffSet html
optimalSurvivalCutoff html
parseASeventNames html
parseCategoricalGroups html
parseDateResponse html
parseFirebrowseMetadata html
parseMatsEvent html
parseMatsGeneric html
parseMisoAnnotation html
parseMisoEvent html
parseMisoEventID html
parseMisoGeneric html
parseMisoId html
parseSplicingEvent html
parseSuppaEvent html
parseSuppaGeneric html
parseTcgaSampleInfo html
parseUniprotXML html
parseUrlsFromFirebrowseResponse html
parseValidFile html
parseVastToolsEvent html
parseVastToolsSE html
performICA html
performPCA html
plot.GEandAScorrelation html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plot.GEandAScorrelation.Rd:71: file link 'loess.smooth' in package 'stats' does not exist and so has been treated as a topic
plotClusters html
plotDistribution html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plotDistribution.Rd:34: file link 'density.default' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plotDistribution.Rd:41: file link 'bw.nrd' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/plotDistribution.Rd:89: file link 'approx' in package 'stats' does not exist and so has been treated as a topic
plotGeneExprPerSample html
plotGroupIndependence html
plotICA html
plotPCA html
plotPointsStyle html
plotProtein html
plotRowStats html
plotSingleICA html
plotSplicingEvent 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
processButton html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/processButton.Rd:19: file link 'validateCssUnit' in package 'shiny' does not exist and so has been treated as a topic
processDatasetNames html
processSRAdata 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
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/reduceDimensionality.Rd:25: file link 'as.numeric' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/reduceDimensionality.Rd:26: file link 'is.numeric' in package 'base' does not exist and so has been treated as a topic
renameDuplicated html
renameGroups html
renderBoxplot html
renderDataTableSparklines html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/renderDataTableSparklines.Rd:22: file link 'dataTableOutput' in package 'shiny' does not exist and so has been treated as a topic
renderGeneticInfo html
renderGroupInterface html
renderProteinInfo html
rm.null html
roundDigits html
roundMinDown html
rowMeans html
saveProcessedSRAdata 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
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpu8j28e/R.INSTALL2810305c70c2/psichomics/man/styleModal.Rd:41: file link 'removeModal' in package 'shiny' does not exist and so has been treated as a topic
subjectMultiMatchWarning html
subsetGeneExpressionFromMatchingGenes html
survdiffTerms 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
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'psichomics' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
~~~~^~~~~~~~~~~~
psiFastCalc.cpp:31:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-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 of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
~~~~^~~~~~~~~~~~
psiFastCalc.cpp:63:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (size_t idx=0; idx < inc.length(); idx++) {
~~~~^~~~~~~~~~~~~~
psiFastCalc.cpp:66:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (size_t k=0; k < incIdx.length(); k++)
~~^~~~~~~~~~~~~~~~~
psiFastCalc.cpp:71:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (size_t k=0; k < excIdx.length(); k++)
~~^~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psichomics' as psichomics_1.14.1.zip
* DONE (psichomics)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'psichomics' successfully unpacked and MD5 sums checked
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psichomics.Rcheck/tests_i386/spelling.Rout
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.20 0.00 0.92
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psichomics.Rcheck/tests_x64/spelling.Rout
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.20 0.07 0.26
|
|
psichomics.Rcheck/tests_i386/testthat.Rout
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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: 1240 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
27.09 2.39 35.23
|
psichomics.Rcheck/tests_x64/testthat.Rout
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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: 1240 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
25.67 0.98 32.46
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psichomics.Rcheck/examples_i386/psichomics-Ex.timings
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psichomics.Rcheck/examples_x64/psichomics-Ex.timings
|