Nuno Saraiva-Agostinho
| Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/psichomics |
| git_branch: devel |
| git_last_commit: 55e72bb |
| git_last_commit_date: 2024-10-29 10:15:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
| 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 1603/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.33.0 (landing page) Nuno Saraiva-Agostinho
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: psichomics |
| Version: 1.33.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings psichomics_1.33.0.tar.gz |
| StartedAt: 2024-12-23 10:55:45 -0000 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 11:06:40 -0000 (Mon, 23 Dec 2024) |
| EllapsedTime: 654.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: psichomics.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings psichomics_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.33.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘psichomics’ can be installed ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/psichomics.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
Warning: program compiled against libxml 212 using older 211
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
colSums-EList-method.Rd: EList-class
renderDataTableSparklines.Rd: renderDataTable
showAlert.Rd: showModal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* 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.
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
convertGeneIdentifiers 19.217 2.234 30.271
listSplicingAnnotations 13.942 0.950 20.855
loadAnnotation 3.642 0.738 6.179
listAllAnnotations 3.199 0.231 5.072
queryEnsemblByGene 0.124 0.000 6.595
* 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: 5 WARNINGs, 9 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/psichomics.Rcheck/00check.log’
for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c progressBar.cpp -o progressBar.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c psiFastCalc.cpp -o psiFastCalc.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c vastToolsParser.cpp -o vastToolsParser.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-psichomics/00new/psichomics/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 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 Warning: program compiled against libxml 212 using older 211 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (psichomics)
psichomics.Rcheck/tests/spelling.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
0.181 0.055 0.226
psichomics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
Warning: program compiled against libxml 212 using older 211
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
psichomics 1.33.0: 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
31.494 1.996 42.199
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0 | 0 | 0 | |
| assignValuePerSubject | 0.008 | 0.014 | 0.024 | |
| blendColours | 0.001 | 0.000 | 0.001 | |
| calculateLoadingsContribution | 0.008 | 0.004 | 0.017 | |
| convertGeneIdentifiers | 19.217 | 2.234 | 30.271 | |
| correlateGEandAS | 0.019 | 0.007 | 0.028 | |
| createGroupByAttribute | 0.001 | 0.000 | 0.002 | |
| createJunctionsTemplate | 0.002 | 0.000 | 0.003 | |
| customRowMeans | 0.001 | 0.000 | 0.001 | |
| diffAnalyses | 0.109 | 0.007 | 0.118 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.027 | 0.004 | 1.869 | |
| filterGeneExpr | 0.009 | 0.000 | 0.009 | |
| filterGroups | 0.002 | 0.000 | 0.002 | |
| filterPSI | 0.020 | 0.000 | 0.019 | |
| getAttributesTime | 0.004 | 0.000 | 0.004 | |
| getDownloadsFolder | 0.000 | 0.000 | 0.001 | |
| getFirebrowseDateFormat | 0.000 | 0.000 | 0.001 | |
| getGeneList | 0.004 | 0.000 | 0.005 | |
| getGtexDataTypes | 0.000 | 0.000 | 0.001 | |
| getGtexTissues | 0 | 0 | 0 | |
| getNumerics | 0.002 | 0.000 | 0.003 | |
| getSampleFromSubject | 0.001 | 0.000 | 0.002 | |
| getSplicingEventFromGenes | 0.005 | 0.000 | 0.005 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getSubjectFromSample | 0.001 | 0.000 | 0.000 | |
| getTCGAdataTypes | 0.024 | 0.016 | 1.478 | |
| getValidEvents | 0.004 | 0.000 | 0.004 | |
| groupPerElem | 0.001 | 0.000 | 0.001 | |
| hchart.survfit | 0.336 | 0.051 | 0.449 | |
| isFirebrowseUp | 0.007 | 0.000 | 0.245 | |
| labelBasedOnCutoff | 0.000 | 0.000 | 0.001 | |
| leveneTest | 0.01 | 0.00 | 0.01 | |
| listAllAnnotations | 3.199 | 0.231 | 5.072 | |
| listSplicingAnnotations | 13.942 | 0.950 | 20.855 | |
| loadAnnotation | 3.642 | 0.738 | 6.179 | |
| loadGtexData | 0 | 0 | 0 | |
| loadLocalFiles | 0 | 0 | 0 | |
| loadSRAproject | 0 | 0 | 0 | |
| loadTCGAdata | 0.008 | 0.012 | 0.496 | |
| missingDataModal | 0 | 0 | 0 | |
| normaliseGeneExpression | 0.038 | 0.008 | 0.046 | |
| optimalSurvivalCutoff | 0.159 | 0.052 | 0.212 | |
| parseCategoricalGroups | 0.002 | 0.000 | 0.002 | |
| parseFirebrowseMetadata | 0.048 | 0.020 | 1.266 | |
| parseMatsEvent | 0.004 | 0.004 | 0.007 | |
| parseMatsGeneric | 0.032 | 0.000 | 0.031 | |
| parseMisoAnnotation | 0.237 | 0.123 | 0.378 | |
| parseMisoEvent | 0.002 | 0.004 | 0.006 | |
| parseMisoEventID | 0.006 | 0.004 | 0.012 | |
| parseMisoGeneric | 0.049 | 0.000 | 0.049 | |
| parseMisoId | 0.001 | 0.000 | 0.000 | |
| parseSplicingEvent | 0.006 | 0.000 | 0.006 | |
| parseSuppaEvent | 0.006 | 0.000 | 0.005 | |
| parseSuppaGeneric | 0.025 | 0.000 | 0.025 | |
| parseTcgaSampleInfo | 0.005 | 0.000 | 0.007 | |
| parseUrlsFromFirebrowseResponse | 0.040 | 0.000 | 0.796 | |
| parseVastToolsEvent | 0.007 | 0.000 | 0.008 | |
| parseVastToolsSE | 0.024 | 0.000 | 0.025 | |
| performICA | 0.008 | 0.000 | 0.008 | |
| performPCA | 0.002 | 0.000 | 0.002 | |
| plot.GEandAScorrelation | 0.753 | 0.108 | 0.862 | |
| plotDistribution | 0.995 | 0.159 | 1.158 | |
| plotGeneExprPerSample | 0.110 | 0.028 | 0.138 | |
| plotGroupIndependence | 0.207 | 0.048 | 0.255 | |
| plotICA | 0.179 | 0.032 | 0.218 | |
| plotLibrarySize | 0.331 | 0.060 | 0.391 | |
| plotPCA | 0.346 | 0.056 | 0.403 | |
| plotPCAvariance | 0.066 | 0.004 | 0.070 | |
| plotProtein | 0.853 | 0.028 | 2.483 | |
| plotRowStats | 0.613 | 0.004 | 0.619 | |
| plotSingleICA | 0.242 | 0.024 | 0.268 | |
| plotSplicingEvent | 0.103 | 0.000 | 0.103 | |
| plotSurvivalCurves | 0.121 | 0.004 | 0.126 | |
| plotSurvivalPvaluesByCutoff | 0.724 | 0.004 | 0.729 | |
| plotTranscripts | 0.022 | 0.004 | 1.873 | |
| prepareAnnotationFromEvents | 0.221 | 0.004 | 0.225 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| prepareJunctionQuantSTAR | 0 | 0 | 0 | |
| prepareSRAmetadata | 0 | 0 | 0 | |
| processSurvTerms | 0.012 | 0.000 | 0.011 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.014 | 0.000 | 0.014 | |
| queryEnsembl | 0.036 | 0.004 | 1.039 | |
| queryEnsemblByGene | 0.124 | 0.000 | 6.595 | |
| queryFirebrowseData | 0.046 | 0.008 | 1.585 | |
| queryPubMed | 0.036 | 0.004 | 3.726 | |
| queryUniprot | 0.047 | 0.001 | 0.788 | |
| readFile | 0.000 | 0.001 | 0.001 | |
| renameDuplicated | 0.000 | 0.000 | 0.001 | |
| renderBoxplot | 0.140 | 0.012 | 0.153 | |
| survdiffTerms | 0.008 | 0.000 | 0.008 | |
| survfit.survTerms | 0.03 | 0.00 | 0.03 | |
| testGroupIndependence | 0.004 | 0.000 | 0.004 | |
| testSurvival | 0.028 | 0.000 | 0.028 | |
| textSuggestions | 0.001 | 0.000 | 0.000 | |
| trimWhitespace | 0 | 0 | 0 | |