| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:33 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 1101/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IsoformSwitchAnalyzeR 2.13.0 (landing page) Kristoffer Vitting-Seerup
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
| See other builds for IsoformSwitchAnalyzeR in R Universe. | ||||||||||||||
|
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: 2.13.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.13.0.tar.gz |
| StartedAt: 2026-05-06 01:02:54 -0400 (Wed, 06 May 2026) |
| EndedAt: 2026-05-06 01:35:00 -0400 (Wed, 06 May 2026) |
| EllapsedTime: 1926.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.13.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-06 05:02:56 UTC
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.13.0’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
installed size is 7.5Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 1.1Mb
extdata 4.9Mb
* 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 loading without being on the library search path ... 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
IsoformSwitchTestDEXSeq 181.218 1.777 182.968
IsoformSwitchTestSatuRn 152.452 1.735 155.369
importSalmonData 118.545 1.110 130.106
prepareSalmonFilesDataFrame 104.599 0.554 108.894
switchAnalyzeRlist 84.548 0.380 84.894
importRdata 78.705 0.409 80.506
isoformToGeneExp 74.878 0.376 75.220
isoformSwitchAnalysisCombined 37.378 1.462 38.841
extractSequence 14.797 0.012 14.809
analyzeORF 14.398 0.070 14.468
extractTopSwitches 14.337 0.039 14.377
extractSwitchSummary 14.195 0.026 14.222
preFilter 6.954 0.037 6.991
switchPlot 6.007 0.161 6.168
analyzeAlternativSplicing 6.008 0.003 6.011
isoformSwitchAnalysisPart1 5.913 0.001 5.914
extractGenomeWideSplicingAnalysis 5.282 0.059 5.341
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.24-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** this is package ‘IsoformSwitchAnalyzeR’ version ‘2.13.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.24-bioc/R/site-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 | 181.218 | 1.777 | 182.968 | |
| IsoformSwitchTestSatuRn | 152.452 | 1.735 | 155.369 | |
| addORFfromGTF | 0.788 | 0.007 | 0.794 | |
| analyzeAlternativSplicing | 6.008 | 0.003 | 6.011 | |
| analyzeCPAT | 0.054 | 0.000 | 0.054 | |
| analyzeCPC2 | 0.050 | 0.001 | 0.051 | |
| analyzeDeepLoc2 | 0.187 | 0.040 | 0.215 | |
| analyzeDeepTMHMM | 0.435 | 0.014 | 0.449 | |
| analyzeIUPred2A | 2.337 | 0.053 | 2.390 | |
| analyzeNovelIsoformORF | 0.603 | 0.002 | 0.605 | |
| analyzeORF | 14.398 | 0.070 | 14.468 | |
| analyzePFAM | 0.425 | 0.005 | 0.431 | |
| analyzeSignalP | 0.085 | 0.000 | 0.086 | |
| analyzeSwitchConsequences | 1.238 | 0.007 | 1.246 | |
| exportToPairedGSEA | 0.012 | 0.002 | 0.015 | |
| expressionAnalysisPlots | 1.624 | 0.057 | 1.681 | |
| extractConsequenceEnrichment | 0.626 | 0.014 | 0.641 | |
| extractConsequenceEnrichmentComparison | 0.877 | 0.005 | 0.882 | |
| extractConsequenceSummary | 1.015 | 0.004 | 1.020 | |
| extractGeneExpression | 0.042 | 0.001 | 0.044 | |
| extractGenomeWideAnalysis | 4.555 | 0.086 | 4.641 | |
| extractGenomeWideSplicingAnalysis | 5.282 | 0.059 | 5.341 | |
| extractSequence | 14.797 | 0.012 | 14.809 | |
| extractSplicingEnrichment | 1.217 | 0.003 | 1.220 | |
| extractSplicingEnrichmentComparison | 1.421 | 0.004 | 1.424 | |
| extractSplicingSummary | 1.311 | 0.000 | 1.312 | |
| extractSwitchOverlap | 0.349 | 0.002 | 0.352 | |
| extractSwitchSummary | 14.195 | 0.026 | 14.222 | |
| extractTopSwitches | 14.337 | 0.039 | 14.377 | |
| importCufflinksGalaxyData | 0.000 | 0.000 | 0.001 | |
| importGTF | 0.799 | 0.017 | 0.815 | |
| importIsoformExpression | 0.603 | 0.159 | 0.705 | |
| importRdata | 78.705 | 0.409 | 80.506 | |
| importSalmonData | 118.545 | 1.110 | 130.106 | |
| isoformSwitchAnalysisCombined | 37.378 | 1.462 | 38.841 | |
| isoformSwitchAnalysisPart1 | 5.913 | 0.001 | 5.914 | |
| isoformSwitchAnalysisPart2 | 4.572 | 0.167 | 4.727 | |
| isoformToGeneExp | 74.878 | 0.376 | 75.220 | |
| isoformToIsoformFraction | 0.193 | 0.090 | 0.249 | |
| preFilter | 6.954 | 0.037 | 6.991 | |
| prepareSalmonFilesDataFrame | 104.599 | 0.554 | 108.894 | |
| subsetSwitchAnalyzeRlist | 0.026 | 0.001 | 0.027 | |
| switchAnalyzeRlist | 84.548 | 0.380 | 84.894 | |
| switchPlot | 6.007 | 0.161 | 6.168 | |
| switchPlotTranscript | 1.961 | 0.001 | 1.963 | |
| testData | 0.012 | 0.001 | 0.014 | |