| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:39:44 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 1596/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.29.1 (landing page) Nuno Saraiva-Agostinho
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.29.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.29.1.tar.gz |
| StartedAt: 2024-03-02 08:50:23 -0500 (Sat, 02 Mar 2024) |
| EndedAt: 2024-03-02 09:14:37 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 1453.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: psichomics.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.29.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.29.1’
* 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 ... 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 ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘psichomics-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parseUrlsFromFirebrowseResponse
> ### Title: Retrieve URLs from a response to a FireBrowse data query
> ### Aliases: parseUrlsFromFirebrowseResponse
> ### Keywords: internal
>
> ### ** Examples
>
> res <- psichomics:::queryFirebrowseData(cohort = "ACC")
Error in `[[.default`(getTCGAdates(), 1) : subscript out of bounds
Calls: <Anonymous> -> [[ -> [[.Date -> .Date -> NextMethod
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
`parsed` inherits from `'NULL'` not `'character'`.
── Failure ('testFirebrowse.R:89:5'): getFirebrowseCohorts obtains the cohorts available ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFirebrowse.R:94:5'): getFirebrowseCohorts obtains the cohorts available ──
`parsed` inherits from `'NULL'` not `'character'`.
── Failure ('testFirebrowse.R:95:5'): getFirebrowseCohorts obtains the cohorts available ──
`parsed` not equal to c(ACC = "Adrenocortical carcinoma", LGG = "Brain Lower Grade Glioma").
target is NULL, current is character
[ FAIL 8 | WARN 0 | SKIP 5 | PASS 1394 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck/00check.log’
for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progressBar.cpp -o progressBar.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c psiFastCalc.cpp -o psiFastCalc.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vastToolsParser.cpp -o vastToolsParser.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-psichomics/00new/psichomics/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
0.354 0.117 0.455
psichomics.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 1.29.1: 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 8 | WARN 0 | SKIP 5 | PASS 1394 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• Could not resolve host name (1): 'testFirebrowse.R:110:9'
• 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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testFirebrowse.R:31:5'): queryFirebrowseData queries the Firebrowse web API ──
<subscriptOutOfBoundsError/error/condition>
Error in ``[[.default`(getTCGAdates(), 1)`: subscript out of bounds
Backtrace:
▆
1. └─psichomics:::queryFirebrowseData(cohort = cohort) at testFirebrowse.R:31:5
2. ├─getTCGAdates()[[1]]
3. ├─base::`[[.Date`(getTCGAdates(), 1)
4. │ └─base::.Date(NextMethod("[["), oldClass(x))
5. └─base::NextMethod("[[")
── Failure ('testFirebrowse.R:57:5'): parseFirebrowseMetadata parses metadata from Firebrowse ──
parsed[[1]] inherits from `'character'` not `'character'`.
── Error ('testFirebrowse.R:59:5'): parseFirebrowseMetadata parses metadata from Firebrowse ──
Error in `parsed[[1]][, 1]`: incorrect number of dimensions
Backtrace:
▆
1. ├─testthat::expect_true(all(cohorts %in% parsed[[1]][, 1])) at testFirebrowse.R:59:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cohorts %in% parsed[[1]][, 1]
── Failure ('testFirebrowse.R:81:5'): getFirebrowseDates obtains the datestamps of the data available ──
all(dates %in% as.character(resp)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFirebrowse.R:88:5'): getFirebrowseCohorts obtains the cohorts available ──
`parsed` inherits from `'NULL'` not `'character'`.
── Failure ('testFirebrowse.R:89:5'): getFirebrowseCohorts obtains the cohorts available ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFirebrowse.R:94:5'): getFirebrowseCohorts obtains the cohorts available ──
`parsed` inherits from `'NULL'` not `'character'`.
── Failure ('testFirebrowse.R:95:5'): getFirebrowseCohorts obtains the cohorts available ──
`parsed` not equal to c(ACC = "Adrenocortical carcinoma", LGG = "Brain Lower Grade Glioma").
target is NULL, current is character
[ FAIL 8 | WARN 0 | SKIP 5 | PASS 1394 ]
Error: Test failures
Execution halted
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.001 | 0.001 | 0.002 | |
| assignValuePerSubject | 0.035 | 0.019 | 0.067 | |
| blendColours | 0.001 | 0.000 | 0.002 | |
| calculateLoadingsContribution | 0.016 | 0.005 | 0.028 | |
| convertGeneIdentifiers | 25.572 | 2.096 | 35.165 | |
| correlateGEandAS | 0.036 | 0.014 | 0.057 | |
| createGroupByAttribute | 0.002 | 0.001 | 0.003 | |
| createJunctionsTemplate | 0.004 | 0.002 | 0.008 | |
| customRowMeans | 0.001 | 0.001 | 0.006 | |
| diffAnalyses | 0.161 | 0.019 | 0.207 | |
| downloadFiles | 0.000 | 0.001 | 0.001 | |
| ensemblToUniprot | 0.032 | 0.003 | 6.973 | |
| filterGeneExpr | 0.013 | 0.003 | 0.016 | |
| filterGroups | 0.002 | 0.001 | 0.003 | |
| filterPSI | 0.028 | 0.009 | 0.037 | |
| getAttributesTime | 0.005 | 0.001 | 0.006 | |
| getDownloadsFolder | 0.000 | 0.001 | 0.001 | |
| getFirebrowseDateFormat | 0.000 | 0.001 | 0.001 | |
| getGeneList | 0.006 | 0.002 | 0.008 | |
| getGtexDataTypes | 0.001 | 0.001 | 0.002 | |
| getGtexTissues | 0.000 | 0.000 | 0.001 | |
| getNumerics | 0.004 | 0.001 | 0.005 | |
| getSampleFromSubject | 0.001 | 0.001 | 0.003 | |
| getSplicingEventFromGenes | 0.007 | 0.002 | 0.008 | |
| getSplicingEventTypes | 0.001 | 0.001 | 0.002 | |
| getSubjectFromSample | 0.001 | 0.001 | 0.001 | |
| getTCGAdataTypes | 0.043 | 0.006 | 60.383 | |
| getValidEvents | 0.007 | 0.004 | 0.011 | |
| groupPerElem | 0.001 | 0.001 | 0.002 | |
| hchart.survfit | 0.541 | 0.231 | 1.017 | |
| isFirebrowseUp | 0.010 | 0.001 | 0.061 | |
| labelBasedOnCutoff | 0.001 | 0.001 | 0.002 | |
| leveneTest | 0.016 | 0.001 | 0.020 | |
| listAllAnnotations | 5.645 | 0.534 | 14.373 | |
| listSplicingAnnotations | 21.335 | 2.107 | 28.844 | |
| loadAnnotation | 5.506 | 0.521 | 7.250 | |
| loadGtexData | 0.001 | 0.001 | 0.001 | |
| loadLocalFiles | 0.000 | 0.001 | 0.000 | |
| loadSRAproject | 0.000 | 0.000 | 0.001 | |
| loadTCGAdata | 0.012 | 0.003 | 30.401 | |
| missingDataModal | 0.000 | 0.000 | 0.001 | |
| normaliseGeneExpression | 0.040 | 0.004 | 0.044 | |
| optimalSurvivalCutoff | 0.199 | 0.003 | 0.202 | |
| parseCategoricalGroups | 0.002 | 0.000 | 0.003 | |
| parseFirebrowseMetadata | 0.056 | 0.009 | 120.995 | |
| parseMatsEvent | 0.010 | 0.002 | 0.012 | |
| parseMatsGeneric | 0.044 | 0.007 | 0.051 | |
| parseMisoAnnotation | 0.290 | 0.024 | 0.339 | |
| parseMisoEvent | 0.009 | 0.002 | 0.015 | |
| parseMisoEventID | 0.012 | 0.005 | 0.020 | |
| parseMisoGeneric | 0.073 | 0.012 | 0.148 | |
| parseMisoId | 0.001 | 0.000 | 0.002 | |
| parseSplicingEvent | 0.010 | 0.006 | 0.026 | |
| parseSuppaEvent | 0.009 | 0.002 | 0.010 | |
| parseSuppaGeneric | 0.044 | 0.006 | 0.075 | |
| parseTcgaSampleInfo | 0.008 | 0.003 | 0.019 | |