##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EventPointer_3.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/EventPointer.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 ‘EventPointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EventPointer’ version ‘3.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 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 ‘EventPointer’ 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 26.7Mb
  sub-directories of 1Mb or more:
    extdata  25.7Mb
* 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 ... WARNING
'::' or ':::' import not declared from: ‘Biobase’
'library' or 'require' calls not declared from:
  ‘data.table’ ‘doParallel’
'library' or 'require' calls in package code:
  ‘data.table’ ‘doParallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
  ‘GenomicAlignments:::findSpliceOverlaps’
  ‘limma:::normalizeBetweenArrays’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘SGSeq:::XS2strand’ ‘SGSeq:::addFeatureID’ ‘SGSeq:::addGeneID’
  ‘SGSeq:::checkApplyResultsForErrors’ ‘SGSeq:::checkBamInfo’
  ‘SGSeq:::checkSampleInfo’ ‘SGSeq:::completeMcols’
  ‘SGSeq:::convertFpkmToCount’ ‘SGSeq:::edges’ ‘SGSeq:::exonGraph’
  ‘SGSeq:::extractRangesFromFeatures’ ‘SGSeq:::feature2name’
  ‘SGSeq:::filterGap’ ‘SGSeq:::generateWarningMessage’
  ‘SGSeq:::matchSGFeatures’ ‘SGSeq:::nodes’ ‘SGSeq:::pfirst’
  ‘SGSeq:::plast’ ‘SGSeq:::propagateAnnotation’ ‘SGSeq:::propagateXS’
  ‘SGSeq:::rbindDfsWithoutRowNames’ ‘SGSeq:::splitCharacterList’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
EventDetection_transcriptome: no visible binding for global variable
  ‘jj’
EventPointerStats_BAM: no visible global function definition for
  ‘write.csv’
EventPointerStats_ST: no visible global function definition for
  ‘write.csv’
EventsDetection_BAM: no visible global function definition for
  ‘write.csv’
SF_Prediction: no visible binding for global variable ‘valueRanking’
SF_Prediction: no visible binding for global variable ‘PSI_table’
annotate2: no visible global function definition for
  ‘addDummySpliceSites’
annotate2: no visible global function definition for ‘annotatePaths’
annotateFeatures2: no visible global function definition for
  ‘matchTxFeatures’
calcBootstrapPSI : <anonymous>: no visible global function definition
  for ‘rmultinom’
callGRseq_parallel: no visible binding for global variable ‘i’
call_get_table_Bootstrap: no visible binding for global variable ‘ii’
constructGRangesFromRanges: no visible global function definition for
  ‘endoapply’
estimateAbsoluteConc_boot: no visible global function definition for
  ‘matnnls’
fitgl: no visible binding for global variable ‘hist’
fragExonIntron: no visible global function definition for ‘gr2co’
fragExonIntron: no visible binding for global variable ‘sample_name’
generateWarningMessage: no visible global function definition for
  ‘makeWarningMessage’
myphyper: no visible global function definition for ‘dhyper’
predictTxFeaturesTotal: no visible global function definition for
  ‘generateCompleteMessage’
predictTxFeaturesTotal: no visible global function definition for
  ‘gr2co’
processCounts: no visible global function definition for ‘endoapply’
processCounts: no visible global function definition for
  ‘generateCompleteMessage’
processCounts: no visible global function definition for ‘gr2co’
voom2: no visible global function definition for ‘lowess’
voom2: no visible global function definition for ‘title’
voom2: no visible global function definition for ‘lines’
voom2: no visible global function definition for ‘approxfun’
voomEventPointerBAM: no visible global function definition for ‘rowSds’
voomEventPointerBAM: no visible global function definition for ‘lm’
voomEventPointerST : <anonymous>: no visible global function definition
  for ‘colMeans2’
voomEventPointerST: no visible global function definition for ‘rowSds’
voomEventPointerST: no visible global function definition for ‘lm’
Undefined global functions or variables:
  PSI_table addDummySpliceSites annotatePaths approxfun colMeans2
  dhyper endoapply generateCompleteMessage gr2co hist i ii jj lines lm
  lowess makeWarningMessage matchTxFeatures matnnls rmultinom rowSds
  sample_name title valueRanking write.csv
Consider adding
  importFrom("graphics", "hist", "lines", "title")
  importFrom("stats", "approxfun", "dhyper", "lm", "lowess", "rmultinom")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
* 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 ... WARNING
Documented arguments not in \usage in Rd file 'EventPointerBAM_IGV.Rd':
  ‘Events’

Undocumented arguments in Rd file 'InternalFunctions.Rd'
  ‘Events’ ‘PSR_Gene’ ‘Junc_Gene’ ‘Gxx’ ‘paths’ ‘GenI’ ‘SG’ ‘twopaths’
  ‘Signal1’ ‘Signal2’ ‘SignalR’ ‘lambda’ ‘datos’ ‘randSol’ ‘tol’
  ‘Incidence’ ‘sg_txiki’ ‘type’ ‘x’ ‘readsC’ ‘widthinit’ ‘EventInfo’
  ‘SG_Edges’ ‘ExFit’ ‘Result’ ‘l1’ ‘l2’ ‘lR’ ‘CountMatrix’ ‘l1eq’
  ‘l2eq’ ‘lReq’ ‘rowProcess’ ‘PSI_boot’ ‘nboot’ ‘ncol’ ‘Pv1’ ‘t1’ ‘Pv2’
  ‘t2’ ‘coherence’ ‘X’ ‘Y’ ‘Probes’ ‘Class’ ‘Final’ ‘SG_Gene’ ‘PATH’
  ‘Data’ ‘Paths’ ‘file’ ‘chipType’ ‘tags’ ‘rows’ ‘cols’ ‘verbose’
  ‘xynames’ ‘gcol’ ‘ucol’ ‘splitn’ ‘col.class’ ‘Directory’ ‘...’ ‘Info’
  ‘edgetr’ ‘events’ ‘coerce’ ‘merge’ ‘features’ ‘query’ ‘subject’
  ‘min_n_sample’ ‘taqman’ ‘FinalExons’ ‘generaldata’ ‘Dir’ ‘nPrimers’
  ‘Primer3Path’ ‘maxLength’ ‘minsep’ ‘wminsep’ ‘valuethreePpenalty’
  ‘wnpaths’ ‘qualityfilter’ ‘mygenomesequence’ ‘n’ ‘thermo.param’
  ‘settings’ ‘FinalSeq’ ‘nProbes’ ‘namesPath’ ‘decreasing’ ‘wg’ ‘from’
  ‘to’ ‘seq’ ‘threeprimers’ ‘pr’ ‘reverse’ ‘size_range’ ‘Tm’ ‘name’
  ‘sequence_target’ ‘Exons’ ‘D’ ‘minexonlength’ ‘Forward’ ‘FinalInfo’
  ‘Exon1’ ‘Exon2’ ‘distinPrimers’ ‘PrimersTwo’ ‘Primers1’
  ‘commonForward’ ‘commonReverse’ ‘namesRef’ ‘numberOfPaths’
  ‘nprimerstwo’ ‘ED’ ‘wNpaths’ ‘wP12inRef’ ‘Primers2’ ‘Event’
  ‘ncommonForward’ ‘ncommonReverse’ ‘nPrimerstwo’ ‘nExons’
  ‘shortdistpenalty’ ‘Dominants’ ‘nt’ ‘items’ ‘Fdata’ ‘combboots’
  ‘incrPSI_original’ ‘ncontrastes’ ‘PSI_arrayP’ ‘nevents’ ‘totchunk’
  ‘chunk’ ‘nsamples’ ‘V’ ‘nbootin’ ‘PSI_arrayS’ ‘l’ ‘I’ ‘J’ ‘CTEind’
  ‘table’ ‘ncontrast’ ‘C’ ‘PSI_boots’ ‘Design’ ‘Contrast’ ‘cores’ ‘ram’
  ‘nbootstraps’ ‘KallistoBootstrap’ ‘th’ ‘chunklist’ ‘incr_PSI’ ‘A’ ‘B’
  ‘method’ ‘EventsFound’ ‘SG_List’ ‘typeA’ ‘y’ ‘intercept’ ‘weights’
  ‘row.chunk’ ‘family’ ‘start’ ‘etastart’ ‘mustart’ ‘offset’ ‘acc’
  ‘maxit’ ‘k’ ‘sparselim’ ‘camp’ ‘eigendec’ ‘tol.values’ ‘tol.vectors’
  ‘tol.solve’ ‘sparse’ ‘trace’ ‘med’ ‘iqr’ ‘chi’ ‘xi’ ‘inc’ ‘na.rm’ ‘q’
  ‘p’ ‘ExS’ ‘nSel’ ‘P_value_PSI’ ‘significance’ ‘resPred’ ‘N’ ‘cSel’
  ‘PSI_table’ ‘ExprT’ ‘GeneGO’ ‘alternative’ ‘mu’ ‘paired’ ‘exact’
  ‘correct’ ‘conf.int’ ‘conf.level’ ‘nmTopEv’ ‘m’ ‘lower.tail’ ‘log.p’
  ‘mievento’ ‘pp1’ ‘pp2’ ‘ppref’ ‘PSI’ ‘counts’ ‘design’ ‘lib.size’
  ‘normalize.method’ ‘block’ ‘correlation’ ‘span’ ‘plot’ ‘save.plot’
  ‘keepMax’ ‘sample_info’ ‘list_features’ ‘which’ ‘valSample’
  ‘min_anchor’ ‘counts_only’ ‘retain_coverage’ ‘mainCount’ ‘gap’
  ‘strand’ ‘sample_name’ ‘junctions’ ‘frag_exonic’ ‘frag_intron’
  ‘matrix1’ ‘matrix2’ ‘splicesites’ ‘side’ ‘include’ ‘exons’ ‘spliceL’
  ‘spliceR’ ‘out’ ‘query_unlisted’ ‘subject_unlisted’ ‘subject_togroup’
  ‘lenQuery’ ‘lenSubject’ ‘option’ ‘exons_i_frag’ ‘alpha’ ‘psi’ ‘beta’
  ‘gamma’ ‘include_counts’ ‘junctions_only’ ‘min_junction_count’
  ‘max_complexity’ ‘min_overhang’ ‘novo’ ‘range’ ‘bam_index’ ‘sWhich’
  ‘file_bam’ ‘paired_end’ ‘fun_name’ ‘item’ ‘msg’ ‘junctions_df’
  ‘seqlevel’ ‘si’ ‘end’ ‘candidates’ ‘relCov’ ‘islands’ ‘frag_coverage’
  ‘seqname’ ‘seqinfo’ ‘EventsDetection_pred’ ‘EventsDetection_ann’
  ‘PathSamplesAbundance’ ‘region’

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.
S3 methods shown with full name in Rd file 'InternalFunctions.Rd':
  ‘sort.exons’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... 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 ... ERROR
Running examples in ‘EventPointer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ResulTable
> ### Title: ResulTable
> ### Aliases: ResulTable
> 
> ### ** Examples
> 
> 
>      data(PSIss)
>      PSI <- PSIss$PSI
>      
>      Dmatrix <- cbind(1,rep(c(0,1),each=2))
>      Cmatrix <- matrix(c(0,1),nrow=2)
>      
>      Fit <- EventPointer_Bootstraps(PSI = PSI,
+                                     Design = Dmatrix,
+                                     Contrast = Cmatrix,
+                                     cores = 1,
+                                     ram = 1,
+                                     nBootstraps = 10,
+                                     UsePseudoAligBootstrap = TRUE)
Error in EventPointer_Bootstraps(PSI = PSI, Design = Dmatrix, Contrast = Cmatrix,  : 
  unused argument (nBootstraps = 10)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
       test_EventDetection 
  
     test_EventDetection_transcriptome.R 
       test_EventDetection_transcriptome 
  
     test_EventPointer_Bootstraps.R 
       test_EventPointer_Bootstraps 
  
     test_EventPointer_RNASeq_IGV.R 
       test_EventPointer_RNASeq_IGV 
  
  
  Error in BiocGenerics:::testPackage("EventPointer") : 
    unit tests failed for package EventPointer
  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, 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/EventPointer.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EventPointer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘EventPointer’ ...
** this is package ‘EventPointer’ version ‘3.19.0’
** 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 dgl.c -o dgl.o
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 params.c -o params.o
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 pgl.c -o pgl.o
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 qdgl.c -o qdgl.o
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 qgl.c -o qgl.o
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 rgl.c -o rgl.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 EventPointer.so dgl.o params.o pgl.o qdgl.o qgl.o rgl.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-EventPointer/00new/EventPointer/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (EventPointer)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> BiocGenerics:::testPackage("EventPointer")

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Creating SG Information...Creating SG Information...Timing stopped at: 0 0 0.001
Error in checkIdentical("Input field is empty", obs) : FALSE 
 
Timing stopped at: 0 0 0
Error in checkIdentical("not inputFile", obs) : FALSE 
 
Timing stopped at: 0 0 0
Error in checkIdentical("PSI field is empty", obs) : FALSE 
 
Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Timing stopped at: 0 0 0
Error in checkIdentical("Missing alternative splicing events", obs) : 
  FALSE 
 
1 2 3 4 


RUNIT TEST PROTOCOL -- Thu Dec 18 19:44:23 2025 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 4 

 
1 Test Suite : 
EventPointer RUnit Tests - 18 test functions, 0 errors, 4 failures
FAILURE in test_EventDetection: Error in checkIdentical("Input field is empty", obs) : FALSE 
 
FAILURE in test_EventDetection_transcriptome: Error in checkIdentical("not inputFile", obs) : FALSE 
 
FAILURE in test_EventPointer_Bootstraps: Error in checkIdentical("PSI field is empty", obs) : FALSE 
 
FAILURE in test_EventPointer_RNASeq_IGV: Error in checkIdentical("Missing alternative splicing events", obs) : 
  FALSE 
 

Test files with failing tests

   test_EventDetection.R 
     test_EventDetection 

   test_EventDetection_transcriptome.R 
     test_EventDetection_transcriptome 

   test_EventPointer_Bootstraps.R 
     test_EventPointer_Bootstraps 

   test_EventPointer_RNASeq_IGV.R 
     test_EventPointer_RNASeq_IGV 


Error in BiocGenerics:::testPackage("EventPointer") : 
  unit tests failed for package EventPointer
Execution halted