| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-31 11:33 -0400 (Tue, 31 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4606 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4534 |
| 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 1107/2374 | 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 | ERROR | |||||||||
| 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: 2.11.1 |
| 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: 2026-03-30 20:08:44 -0400 (Mon, 30 Mar 2026) |
| EndedAt: 2026-03-30 20:16:51 -0400 (Mon, 30 Mar 2026) |
| EllapsedTime: 486.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-31 00:08:45 UTC
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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
IsoformSwitchTestDEXSeq 57.246 0.268 57.833
IsoformSwitchTestSatuRn 47.741 0.208 48.343
importSalmonData 45.522 0.588 54.862
prepareSalmonFilesDataFrame 34.818 0.296 39.197
switchAnalyzeRlist 26.492 0.165 26.866
isoformToGeneExp 24.888 0.199 25.390
importRdata 24.306 0.101 24.474
isoformSwitchAnalysisCombined 13.697 0.145 13.990
* 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/Resources/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** this is package ‘IsoformSwitchAnalyzeR’ version ‘2.11.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang -arch arm64 -std=gnu23 -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=gnu23 -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/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 | 57.246 | 0.268 | 57.833 | |
| IsoformSwitchTestSatuRn | 47.741 | 0.208 | 48.343 | |
| addORFfromGTF | 0.283 | 0.005 | 0.287 | |
| analyzeAlternativSplicing | 1.998 | 0.005 | 2.004 | |
| analyzeCPAT | 0.021 | 0.002 | 0.023 | |
| analyzeCPC2 | 0.019 | 0.002 | 0.021 | |
| analyzeDeepLoc2 | 0.071 | 0.013 | 0.081 | |
| analyzeDeepTMHMM | 0.145 | 0.003 | 0.154 | |
| analyzeIUPred2A | 0.730 | 0.009 | 0.748 | |
| analyzeNovelIsoformORF | 0.212 | 0.003 | 0.216 | |
| analyzeORF | 4.614 | 0.017 | 4.640 | |
| analyzePFAM | 0.154 | 0.002 | 0.156 | |
| analyzeSignalP | 0.032 | 0.002 | 0.035 | |
| analyzeSwitchConsequences | 0.417 | 0.004 | 0.423 | |
| exportToPairedGSEA | 0.006 | 0.001 | 0.007 | |
| expressionAnalysisPlots | 0.516 | 0.003 | 0.520 | |
| extractConsequenceEnrichment | 0.290 | 0.003 | 0.294 | |
| extractConsequenceEnrichmentComparison | 0.274 | 0.002 | 0.275 | |
| extractConsequenceSummary | 0.341 | 0.002 | 0.345 | |
| extractGeneExpression | 0.015 | 0.001 | 0.017 | |
| extractGenomeWideAnalysis | 1.669 | 0.027 | 1.698 | |
| extractGenomeWideSplicingAnalysis | 1.088 | 0.026 | 1.151 | |
| extractSequence | 4.709 | 0.034 | 4.803 | |
| extractSplicingEnrichment | 0.447 | 0.011 | 0.458 | |
| extractSplicingEnrichmentComparison | 0.501 | 0.005 | 0.507 | |
| extractSplicingSummary | 0.429 | 0.004 | 0.434 | |
| extractSwitchOverlap | 0.137 | 0.006 | 0.145 | |
| extractSwitchSummary | 4.462 | 0.013 | 4.496 | |
| extractTopSwitches | 4.599 | 0.013 | 4.624 | |
| importCufflinksGalaxyData | 0 | 0 | 0 | |
| importGTF | 0.278 | 0.003 | 0.281 | |
| importIsoformExpression | 0.241 | 0.049 | 0.259 | |
| importRdata | 24.306 | 0.101 | 24.474 | |
| importSalmonData | 45.522 | 0.588 | 54.862 | |
| isoformSwitchAnalysisCombined | 13.697 | 0.145 | 13.990 | |
| isoformSwitchAnalysisPart1 | 1.869 | 0.006 | 1.882 | |
| isoformSwitchAnalysisPart2 | 1.667 | 0.027 | 1.700 | |
| isoformToGeneExp | 24.888 | 0.199 | 25.390 | |
| isoformToIsoformFraction | 0.084 | 0.038 | 0.103 | |
| preFilter | 2.179 | 0.012 | 2.197 | |
| prepareSalmonFilesDataFrame | 34.818 | 0.296 | 39.197 | |
| subsetSwitchAnalyzeRlist | 0.009 | 0.001 | 0.010 | |
| switchAnalyzeRlist | 26.492 | 0.165 | 26.866 | |
| switchPlot | 1.295 | 0.006 | 1.305 | |
| switchPlotTranscript | 0.653 | 0.004 | 0.659 | |
| testData | 0.005 | 0.002 | 0.007 | |