| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-03 11:35 -0500 (Wed, 03 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4575 |
| 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 1087/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IsoformSwitchAnalyzeR 2.11.1 (landing page) Kristoffer Vitting-Seerup
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK |  | ||||||||
|
To the developers/maintainers of the IsoformSwitchAnalyzeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IsoformSwitchAnalyzeR.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: IsoformSwitchAnalyzeR |
| Version: 2.11.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IsoformSwitchAnalyzeR_2.11.1.tar.gz |
| StartedAt: 2025-12-02 20:38:12 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 20:43:16 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 305.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IsoformSwitchAnalyzeR_2.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.11.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
'limma', 'DEXSeq', 'satuRn', 'sva', 'ggplot2', 'pfamAnalyzeR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Imports includes 30 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IsoformSwitchAnalyzeR’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
installed size is 7.4Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 1.1Mb
extdata 4.8Mb
* 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 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 ... NOTE
analyzeNetSurfP3 : <anonymous>: no visible binding for global variable
'id'
analyzeNovelIsoformORF: no visible binding for global variable
'orf_origin'
analyzeNovelIsoformORF: no visible binding for global variable
'orfStartGenomic'
analyzeNovelIsoformORF: no visible binding for global variable
'isoform_id'
analyzeNovelIsoformORF: no visible binding for global variable
'orfEndGenomic'
expressionAnalysisPlot: no visible binding for global variable
'Condition'
expressionAnalysisPlot: no visible binding for global variable
'gene_expression'
expressionAnalysisPlot: no visible binding for global variable 'CI_up'
expressionAnalysisPlot: no visible binding for global variable
'CI_down'
expressionAnalysisPlot: no visible binding for global variable
'sigLevelPos'
expressionAnalysisPlot: no visible binding for global variable
'sigLevel'
expressionAnalysisPlot: no visible binding for global variable 'CI_hi'
expressionAnalysisPlot: no visible binding for global variable 'CI_low'
expressionAnalysisPlot: no visible binding for global variable 'ymax'
expressionAnalysisPlot: no visible binding for global variable
'sigEval'
expressionAnalysisPlot: no visible binding for global variable 'idNr'
expressionAnalysisPlot: no visible binding for global variable 'IF'
extractConsequenceEnrichment: no visible binding for global variable
'feature2'
extractConsequenceEnrichment: no visible binding for global variable
'propOfRelevantEvents'
extractConsequenceEnrichment: no visible binding for global variable
'Significant'
extractConsequenceEnrichment: no visible binding for global variable
'propCiLo'
extractConsequenceEnrichment: no visible binding for global variable
'propCiHi'
extractConsequenceEnrichment: no visible binding for global variable
'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
variable 'Comparison'
extractConsequenceEnrichmentComparison: no visible binding for global
variable 'propOfRelevantEvents'
extractConsequenceEnrichmentComparison: no visible binding for global
variable 'Significant'
extractConsequenceEnrichmentComparison: no visible binding for global
variable 'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
variable 'propCiHi'
extractConsequenceEnrichmentComparison: no visible binding for global
variable 'propCiLo'
extractConsequenceGenomeWide: no visible binding for global variable
'isoform_feature'
extractConsequenceGenomeWide: no visible binding for global variable
'value'
extractConsequenceGenomeWide: no visible binding for global variable
'variable'
extractConsequenceGenomeWide: no visible binding for global variable
'ymax'
extractConsequenceGenomeWide: no visible binding for global variable
'significance'
extractConsequenceGenomeWide: no visible binding for global variable
'idNr'
extractConsequenceSummary: no visible binding for global variable
'switchConsequence'
extractConsequenceSummary: no visible binding for global variable
'geneFraction'
extractConsequenceSummary: no visible binding for global variable
'nrGenesWithConsequences'
extractConsequenceSummary: no visible binding for global variable
'isoFraction'
extractConsequenceSummary: no visible binding for global variable
'nrIsoWithConsequences'
extractSplicingEnrichment: no visible binding for global variable
'AStype'
extractSplicingEnrichment: no visible binding for global variable
'propUp'
extractSplicingEnrichment: no visible binding for global variable
'Significant'
extractSplicingEnrichment: no visible binding for global variable
'nTot'
extractSplicingEnrichment: no visible binding for global variable
'propUpCiHi'
extractSplicingEnrichment: no visible binding for global variable
'propUpCiLo'
extractSplicingEnrichmentComparison: no visible binding for global
variable 'Comparison'
extractSplicingEnrichmentComparison: no visible binding for global
variable 'propUp'
extractSplicingEnrichmentComparison: no visible binding for global
variable 'Significant'
extractSplicingEnrichmentComparison: no visible binding for global
variable 'nTot'
extractSplicingEnrichmentComparison: no visible binding for global
variable 'propUpCiHi'
extractSplicingEnrichmentComparison: no visible binding for global
variable 'propUpCiLo'
extractSplicingGenomeWide: no visible binding for global variable
'isoform_feature'
extractSplicingGenomeWide: no visible binding for global variable
'value'
extractSplicingGenomeWide: no visible binding for global variable
'variable'
extractSplicingGenomeWide: no visible binding for global variable
'ymax'
extractSplicingGenomeWide: no visible binding for global variable
'significance'
extractSplicingGenomeWide: no visible binding for global variable
'idNr'
extractSplicingSummary: no visible binding for global variable
'splicingResult'
extractSplicingSummary: no visible binding for global variable
'geneFraction'
extractSplicingSummary: no visible binding for global variable
'nrGenesWithConsequences'
extractSplicingSummary: no visible binding for global variable
'isoFraction'
extractSplicingSummary: no visible binding for global variable
'nrIsoWithConsequences'
extractSubCellShifts: no visible binding for global variable 'gene_ref'
extractSubCellShifts: no visible binding for global variable 'gene_id'
extractSubCellShifts: no visible binding for global variable
'condition_1'
extractSubCellShifts: no visible binding for global variable
'condition_2'
extractSubCellShifts: no visible binding for global variable
'isoformUpregulated'
extractSubCellShifts: no visible binding for global variable
'isoformDownregulated'
extractSubCellShifts: no visible binding for global variable
'featureCompared'
extractSubCellShifts: no visible binding for global variable
'isoformsDifferent'
extractSubCellShifts: no visible binding for global variable
'isoform_id'
extractSubCellShifts: no visible binding for global variable
'Localizations'
extractSubCellShifts: no visible binding for global variable
'location_gain'
extractSubCellShifts: no visible binding for global variable
'location_loss'
extractSubCellShifts: no visible binding for global variable 'n_genes'
extractSubCellShifts: no visible binding for global variable 'n_switch'
extractSubCellShifts: no visible binding for global variable 'Genes'
extractSubCellShifts: no visible binding for global variable 'Switch'
importGTF: no visible binding for global variable 'gene_id'
importGTF: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'isoform_id'
importRdata: no visible binding for global variable 'gene_id'
importRdata: no visible binding for global variable 'ref_gene_id'
importRdata: no visible binding for global variable 'n_ref_gene_ids'
importRdata: no visible binding for global variable 'n_iso_na'
importRdata: no visible binding for global variable 'novel_iso'
importRdata: no visible binding for global variable 'known_ref_gene_id'
importRdata: no visible binding for global variable 'nt_overlap'
importRdata: no visible binding for global variable 'frac_overlap'
importRdata: no visible binding for global variable
'log2_overlap_ratio'
importRdata: no visible binding for global variable 'has_ref_gene_id'
importRdata: no visible binding for global variable 'has_novel_iso'
importRdata: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'n_ref'
isoformSwitchAnalysisPart2: no visible global function definition for
'analyzeNetSurfP2'
isoformToGeneExp: no visible binding for global variable 'gene_id'
isoformToGeneExp: no visible binding for global variable 'gene_name'
preFilter: no visible global function definition for 'rename_with'
preFilter: no visible binding for global variable 'isoform_id'
preFilter: no visible global function definition for 'inner_join'
preFilter: no visible binding for global variable 'condition_1'
preFilter: no visible binding for global variable 'condition_2'
preFilter : filter_comparison: no visible binding for global variable
'condition'
preFilter : filter_comparison: no visible global function definition
for 'pull'
preFilter : filter_comparison: no visible binding for global variable
'sampleID'
preFilter : filter_comparison: no visible binding for global variable
'condition_1'
preFilter : filter_comparison: no visible binding for global variable
'condition_2'
preFilter : filter_comparison: no visible global function definition
for 'rowwise'
preFilter : filter_comparison: no visible global function definition
for 'across'
preFilter: no visible global function definition for 'rowwise'
preFilter: no visible global function definition for 'do'
preFilter: no visible binding for global variable '.'
preFilter: no visible global function definition for 'ungroup'
switchPlot: no visible binding for global variable 'x'
switchPlot: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'topology'
switchPlotTranscript: no visible binding for global variable 'idNr'
switchPlotTranscript: no visible binding for global variable 'Topology'
switchPlotTranscript: no visible binding for global variable 'topGroup'
switchPlotTranscript: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'yend'
switchPlotTranscript: no visible binding for global variable 'x'
switchPlotTranscript: no visible binding for global variable 'ymin'
switchPlotTranscript: no visible binding for global variable 'xmin'
switchPlotTranscript: no visible binding for global variable 'ymax'
switchPlotTranscript: no visible binding for global variable 'xmax'
switchPlotTranscript: no visible binding for global variable 'Domain'
switchPlotTranscript: no visible binding for global variable 'value'
Undefined global functions or variables:
. AStype CI_down CI_hi CI_low CI_up Comparison Condition Domain Genes
IF Localizations Significant Switch Topology across analyzeNetSurfP2
condition condition_1 condition_2 do feature2 featureCompared
frac_overlap geneFraction gene_expression gene_id gene_name gene_ref
has_novel_iso has_ref_gene_id id idNr inner_join isoFraction
isoformDownregulated isoformUpregulated isoform_feature isoform_id
isoformsDifferent known_ref_gene_id location_gain location_loss
log2_overlap_ratio nTot n_genes n_iso_na n_ref n_ref_gene_ids
n_switch novel_iso nrGenesWithConsequences nrIsoWithConsequences
nt_overlap orfEndGenomic orfStartGenomic orf_origin propCiHi propCiLo
propOfRelevantEvents propUp propUpCiHi propUpCiLo pull ref_gene_id
rename_with rowwise sampleID sigEval sigLevel sigLevelPos
significance splicingResult switchConsequence topGroup topology
ungroup value variable x xmax xmin y yend ymax ymin
* checking Rd files ... NOTE
checkRd: (-1) isoformToGeneExp.Rd:22: Lost braces; missing escapes or markup?
22 | \item{Using the {isoformGeneAnnotation} argument}.
| ^
checkRd: (-1) isoformToIsoformFraction.Rd:23: Lost braces; missing escapes or markup?
23 | \item{Using the {isoformGeneAnnotation} argument}.
| ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
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
importSalmonData 21.474 0.502 35.082
IsoformSwitchTestDEXSeq 18.967 0.209 20.373
isoformSwitchAnalysisCombined 11.038 1.358 13.435
prepareSalmonFilesDataFrame 9.549 0.241 16.005
IsoformSwitchTestSatuRn 7.782 0.073 8.076
* 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 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** this is package ‘IsoformSwitchAnalyzeR’ version ‘2.11.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o IsoformSwitchAnalyzeR.so utils.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (IsoformSwitchAnalyzeR)
IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings
| name | user | system | elapsed | |
| IsoformSwitchTestDEXSeq | 18.967 | 0.209 | 20.373 | |
| IsoformSwitchTestSatuRn | 7.782 | 0.073 | 8.076 | |
| addORFfromGTF | 0.329 | 0.010 | 0.352 | |
| analyzeAlternativSplicing | 2.032 | 0.005 | 2.108 | |
| analyzeCPAT | 0.049 | 0.003 | 0.053 | |
| analyzeCPC2 | 0.020 | 0.002 | 0.034 | |
| analyzeDeepLoc2 | 0.080 | 0.015 | 0.091 | |
| analyzeDeepTMHMM | 0.140 | 0.002 | 0.144 | |
| analyzeIUPred2A | 0.720 | 0.011 | 0.762 | |
| analyzeNovelIsoformORF | 0.214 | 0.004 | 0.225 | |
| analyzeORF | 2.929 | 0.011 | 3.093 | |
| analyzePFAM | 0.149 | 0.002 | 0.162 | |
| analyzeSignalP | 0.032 | 0.003 | 0.037 | |
| analyzeSwitchConsequences | 0.434 | 0.005 | 0.469 | |
| exportToPairedGSEA | 0.006 | 0.002 | 0.009 | |
| expressionAnalysisPlots | 0.532 | 0.004 | 0.569 | |
| extractConsequenceEnrichment | 0.216 | 0.004 | 0.227 | |
| extractConsequenceEnrichmentComparison | 0.354 | 0.013 | 0.411 | |
| extractConsequenceSummary | 0.358 | 0.020 | 0.445 | |
| extractGeneExpression | 0.017 | 0.001 | 0.025 | |
| extractGenomeWideAnalysis | 1.318 | 0.053 | 1.453 | |
| extractGenomeWideSplicingAnalysis | 1.727 | 0.057 | 1.925 | |
| extractSequence | 2.968 | 0.020 | 3.145 | |
| extractSplicingEnrichment | 0.467 | 0.007 | 0.500 | |
| extractSplicingEnrichmentComparison | 0.498 | 0.009 | 0.561 | |
| extractSplicingSummary | 0.435 | 0.005 | 0.453 | |
| extractSwitchOverlap | 0.137 | 0.007 | 0.155 | |
| extractSwitchSummary | 2.773 | 0.027 | 2.989 | |
| extractTopSwitches | 2.782 | 0.007 | 2.962 | |
| importCufflinksGalaxyData | 0.000 | 0.001 | 0.000 | |
| importGTF | 0.295 | 0.005 | 0.308 | |
| importIsoformExpression | 0.267 | 0.063 | 0.334 | |
| importRdata | 4.238 | 0.053 | 4.515 | |
| importSalmonData | 21.474 | 0.502 | 35.082 | |
| isoformSwitchAnalysisCombined | 11.038 | 1.358 | 13.435 | |
| isoformSwitchAnalysisPart1 | 2.351 | 0.052 | 2.497 | |
| isoformSwitchAnalysisPart2 | 1.138 | 0.130 | 1.287 | |
| isoformToGeneExp | 4.557 | 0.091 | 4.851 | |
| isoformToIsoformFraction | 0.108 | 0.039 | 0.144 | |
| preFilter | 0.322 | 0.004 | 0.328 | |
| prepareSalmonFilesDataFrame | 9.549 | 0.241 | 16.005 | |
| subsetSwitchAnalyzeRlist | 0.010 | 0.002 | 0.012 | |
| switchAnalyzeRlist | 4.385 | 0.054 | 4.559 | |
| switchPlot | 1.307 | 0.007 | 1.388 | |
| switchPlotTranscript | 0.630 | 0.004 | 0.691 | |
| testData | 0.006 | 0.002 | 0.008 | |