Nuno Saraiva-Agostinho
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/psichomics |
| git_branch: devel |
| git_last_commit: 1be6848 |
| git_last_commit_date: 2024-04-30 10:54:27 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1581/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.31.0 (landing page) Nuno Saraiva-Agostinho
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the psichomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psichomics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: psichomics |
| Version: 1.31.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings psichomics_1.31.0.tar.gz |
| StartedAt: 2024-07-16 02:56:32 -0400 (Tue, 16 Jul 2024) |
| EndedAt: 2024-07-16 03:04:18 -0400 (Tue, 16 Jul 2024) |
| EllapsedTime: 466.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: psichomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings psichomics_1.31.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'psichomics/DESCRIPTION' ... OK
* this is package 'psichomics' version '1.31.0'
* 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 ... NOTE
Found the following hidden files and directories:
.devcontainer
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'psichomics' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'createSparklines.Rd':
'id'
Documented arguments not in \usage in Rd file 'renderGeneticInfo.Rd':
'ns'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/psichomics/libs/x64/psichomics.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
convertGeneIdentifiers 13.70 1.48 16.01
listSplicingAnnotations 10.00 1.62 11.88
loadAnnotation 5.75 0.34 6.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'spelling.R'
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck/00check.log'
for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'psichomics' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c progressBar.cpp -o progressBar.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c psiFastCalc.cpp -o psiFastCalc.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vastToolsParser.cpp -o vastToolsParser.o g++ -std=gnu++17 -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-psichomics/00new/psichomics/libs/x64 ** 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 *** 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 * DONE (psichomics)
psichomics.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
0.12 0.10 0.18
psichomics.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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)
psichomics 1.31.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
>
> test_check("psichomics")
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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
EXSK
IR
MERGE3m
MIC
MULTI
[ FAIL 0 | WARN 0 | SKIP 4 | PASS 1418 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• Couldn't resolve host name (1): 'testGeneInfo.R:99:5'
• On Bioconductor (2): 'testDiscardLowCoveragePSIs.R:62:5',
'testGeneInfo.R:50:5'
• On CRAN (1): 'testSRAloading.R:4:5'
[ FAIL 0 | WARN 0 | SKIP 4 | PASS 1418 ]
>
> proc.time()
user system elapsed
25.90 2.46 31.18
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0 | 0 | 0 | |
| assignValuePerSubject | 0.00 | 0.01 | 0.02 | |
| blendColours | 0 | 0 | 0 | |
| calculateLoadingsContribution | 0.00 | 0.02 | 0.02 | |
| convertGeneIdentifiers | 13.70 | 1.48 | 16.01 | |
| correlateGEandAS | 0.02 | 0.00 | 0.01 | |
| createGroupByAttribute | 0 | 0 | 0 | |
| createJunctionsTemplate | 0 | 0 | 0 | |
| customRowMeans | 0 | 0 | 0 | |
| diffAnalyses | 0.06 | 0.01 | 0.08 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.02 | 0.00 | 0.41 | |
| filterGeneExpr | 0 | 0 | 0 | |
| filterGroups | 0 | 0 | 0 | |
| filterPSI | 0.01 | 0.00 | 0.01 | |
| getAttributesTime | 0.02 | 0.00 | 0.02 | |
| getDownloadsFolder | 0 | 0 | 0 | |
| getFirebrowseDateFormat | 0 | 0 | 0 | |
| getGeneList | 0 | 0 | 0 | |
| getGtexDataTypes | 0 | 0 | 0 | |
| getGtexTissues | 0 | 0 | 0 | |
| getNumerics | 0 | 0 | 0 | |
| getSampleFromSubject | 0 | 0 | 0 | |
| getSplicingEventFromGenes | 0 | 0 | 0 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getSubjectFromSample | 0 | 0 | 0 | |
| getTCGAdataTypes | 0.07 | 0.00 | 0.28 | |
| getValidEvents | 0 | 0 | 0 | |
| groupPerElem | 0 | 0 | 0 | |
| hchart.survfit | 0.21 | 0.25 | 0.61 | |
| isFirebrowseUp | 0.00 | 0.00 | 0.04 | |
| labelBasedOnCutoff | 0 | 0 | 0 | |
| leveneTest | 0.02 | 0.00 | 0.02 | |
| listAllAnnotations | 1.59 | 0.43 | 2.20 | |
| listSplicingAnnotations | 10.00 | 1.62 | 11.88 | |
| loadAnnotation | 5.75 | 0.34 | 6.22 | |
| loadGtexData | 0 | 0 | 0 | |
| loadLocalFiles | 0 | 0 | 0 | |
| loadSRAproject | 0 | 0 | 0 | |
| loadTCGAdata | 0.00 | 0.00 | 0.08 | |
| missingDataModal | 0 | 0 | 0 | |
| normaliseGeneExpression | 0.04 | 0.00 | 0.03 | |
| optimalSurvivalCutoff | 0.07 | 0.00 | 0.08 | |
| parseCategoricalGroups | 0 | 0 | 0 | |
| parseFirebrowseMetadata | 0.03 | 0.02 | 0.25 | |
| parseMatsEvent | 0.02 | 0.00 | 0.01 | |
| parseMatsGeneric | 0.02 | 0.00 | 0.02 | |
| parseMisoAnnotation | 0.07 | 0.04 | 0.12 | |
| parseMisoEvent | 0 | 0 | 0 | |
| parseMisoEventID | 0 | 0 | 0 | |
| parseMisoGeneric | 0.04 | 0.00 | 0.04 | |
| parseMisoId | 0 | 0 | 0 | |
| parseSplicingEvent | 0 | 0 | 0 | |
| parseSuppaEvent | 0 | 0 | 0 | |
| parseSuppaGeneric | 0 | 0 | 0 | |
| parseTcgaSampleInfo | 0.02 | 0.00 | 0.02 | |
| parseUrlsFromFirebrowseResponse | 0.03 | 0.00 | 0.18 | |
| parseVastToolsEvent | 0 | 0 | 0 | |
| parseVastToolsSE | 0.01 | 0.00 | 0.02 | |
| performICA | 0 | 0 | 0 | |
| performPCA | 0.02 | 0.00 | 0.02 | |
| plot.GEandAScorrelation | 0.41 | 0.08 | 0.48 | |
| plotDistribution | 0.60 | 0.16 | 0.80 | |
| plotGeneExprPerSample | 0.07 | 0.09 | 0.15 | |
| plotGroupIndependence | 1.04 | 0.00 | 1.27 | |
| plotICA | 0.11 | 0.02 | 0.25 | |
| plotLibrarySize | 0.18 | 0.09 | 0.26 | |
| plotPCA | 0.24 | 0.33 | 0.56 | |
| plotPCAvariance | 0.06 | 0.06 | 0.13 | |
| plotProtein | 0.56 | 0.17 | 1.54 | |
| plotRowStats | 0.39 | 0.02 | 0.41 | |
| plotSingleICA | 0.20 | 0.20 | 0.45 | |
| plotSplicingEvent | 0.05 | 0.00 | 0.05 | |
| plotSurvivalCurves | 0.06 | 0.09 | 0.16 | |
| plotSurvivalPvaluesByCutoff | 0.38 | 0.08 | 0.45 | |
| plotTranscripts | 0.29 | 0.00 | 1.06 | |
| prepareAnnotationFromEvents | 0.17 | 0.00 | 0.17 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| prepareJunctionQuantSTAR | 0 | 0 | 0 | |
| prepareSRAmetadata | 0 | 0 | 0 | |
| processSurvTerms | 0 | 0 | 0 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.00 | 0.02 | 0.01 | |
| queryEnsembl | 0.05 | 0.00 | 0.58 | |
| queryEnsemblByGene | 0.09 | 0.00 | 3.09 | |
| queryFirebrowseData | 0.03 | 0.00 | 0.35 | |
| queryPubMed | 0.02 | 0.00 | 1.04 | |
| queryUniprot | 0.08 | 0.00 | 0.47 | |
| readFile | 0 | 0 | 0 | |
| renameDuplicated | 0.01 | 0.00 | 0.02 | |
| renderBoxplot | 0.07 | 0.09 | 0.17 | |
| survdiffTerms | 0 | 0 | 0 | |
| survfit.survTerms | 0.01 | 0.00 | 0.01 | |
| testGroupIndependence | 0 | 0 | 0 | |
| testSurvival | 0.02 | 0.01 | 0.03 | |
| textSuggestions | 0 | 0 | 0 | |
| trimWhitespace | 0 | 0 | 0 | |