| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 1076/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IsoformSwitchAnalyzeR 2.4.0 (landing page) Kristoffer Vitting-Seerup
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 2.4.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.4.0.tar.gz |
| StartedAt: 2024-06-06 00:15:51 -0400 (Thu, 06 Jun 2024) |
| EndedAt: 2024-06-06 00:28:37 -0400 (Thu, 06 Jun 2024) |
| EllapsedTime: 765.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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.
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 1.1Mb
extdata 3.0Mb
* 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
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'
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 'setdff'
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 condition_1 condition_2
feature2 featureCompared frac_overlap geneFraction gene_expression
gene_id gene_name gene_ref has_novel_iso has_ref_gene_id idNr
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 ref_gene_id setdff sigEval sigLevel sigLevelPos
significance splicingResult switchConsequence topGroup topology 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 ... 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
IsoformSwitchTestDEXSeq 66.972 1.736 68.706
isoformSwitchAnalysisCombined 42.133 1.851 43.987
importSalmonData 28.845 1.004 38.943
prepareSalmonFilesDataFrame 13.647 0.449 18.005
extractSequence 9.279 0.056 9.336
analyzeORF 9.051 0.028 9.079
extractTopSwitches 8.079 0.012 8.092
extractSwitchSummary 7.865 0.028 7.894
isoformSwitchAnalysisPart1 7.500 0.008 7.508
analyzeAlternativSplicing 6.179 0.096 6.275
* 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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 | 66.972 | 1.736 | 68.706 | |
| IsoformSwitchTestSatuRn | 2.727 | 0.092 | 2.789 | |
| addORFfromGTF | 0.822 | 0.004 | 0.826 | |
| analyzeAlternativSplicing | 6.179 | 0.096 | 6.275 | |
| analyzeCPAT | 0.052 | 0.008 | 0.063 | |
| analyzeCPC2 | 0.045 | 0.004 | 0.049 | |
| analyzeDeepLoc2 | 0.217 | 0.024 | 0.230 | |
| analyzeDeepTMHMM | 0.476 | 0.004 | 0.481 | |
| analyzeIUPred2A | 2.323 | 0.052 | 2.376 | |
| analyzeNovelIsoformORF | 0.618 | 0.008 | 0.626 | |
| analyzeORF | 9.051 | 0.028 | 9.079 | |
| analyzePFAM | 0.438 | 0.004 | 0.443 | |
| analyzeSignalP | 0.115 | 0.000 | 0.116 | |
| analyzeSwitchConsequences | 0.999 | 0.012 | 1.011 | |
| expressionAnalysisPlots | 1.096 | 0.008 | 1.103 | |
| extractConsequenceEnrichment | 0.447 | 0.004 | 0.452 | |
| extractConsequenceEnrichmentComparison | 0.627 | 0.000 | 0.627 | |
| extractConsequenceSummary | 0.774 | 0.000 | 0.773 | |
| extractGeneExpression | 0.042 | 0.000 | 0.042 | |
| extractGenomeWideAnalysis | 4.556 | 0.140 | 4.696 | |
| extractGenomeWideSplicingAnalysis | 3.801 | 0.092 | 3.893 | |
| extractSequence | 9.279 | 0.056 | 9.336 | |
| extractSplicingEnrichment | 1.076 | 0.013 | 1.089 | |
| extractSplicingEnrichmentComparison | 1.191 | 0.000 | 1.191 | |
| extractSplicingSummary | 0.990 | 0.004 | 0.993 | |
| extractSwitchOverlap | 0.358 | 0.004 | 0.363 | |
| extractSwitchSummary | 7.865 | 0.028 | 7.894 | |
| extractTopSwitches | 8.079 | 0.012 | 8.092 | |
| importCufflinksGalaxyData | 0.000 | 0.000 | 0.001 | |
| importGTF | 0.771 | 0.008 | 0.779 | |
| importIsoformExpression | 0.653 | 0.159 | 0.761 | |
| importRdata | 2.341 | 0.148 | 2.459 | |
| importSalmonData | 28.845 | 1.004 | 38.943 | |
| isoformSwitchAnalysisCombined | 42.133 | 1.851 | 43.987 | |
| isoformSwitchAnalysisPart1 | 7.500 | 0.008 | 7.508 | |
| isoformSwitchAnalysisPart2 | 3.312 | 0.205 | 3.503 | |
| isoformToGeneExp | 2.885 | 0.091 | 2.945 | |
| isoformToIsoformFraction | 0.235 | 0.064 | 0.269 | |
| preFilter | 0.027 | 0.000 | 0.027 | |
| prepareSalmonFilesDataFrame | 13.647 | 0.449 | 18.005 | |
| subsetSwitchAnalyzeRlist | 0.026 | 0.000 | 0.025 | |
| switchAnalyzeRlist | 2.599 | 0.108 | 2.675 | |
| switchPlot | 3.224 | 0.020 | 3.244 | |
| switchPlotTranscript | 1.721 | 0.048 | 1.769 | |
| testData | 0.014 | 0.000 | 0.014 | |