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This page was generated on 2024-06-13 12:18 -0400 (Thu, 13 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4344
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 665/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EventPointer 3.13.0  (landing page)
Juan A. Ferrer-Bonsoms
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/EventPointer
git_branch: devel
git_last_commit: 6c3c36a
git_last_commit_date: 2024-04-30 10:56:34 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for EventPointer on nebbiolo2

To the developers/maintainers of the EventPointer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EventPointer.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.

raw results


Summary

Package: EventPointer
Version: 3.13.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EventPointer_3.13.0.tar.gz
StartedAt: 2024-06-12 22:59:05 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 23:05:00 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 354.7 seconds
RetCode: 0
Status:   OK  
CheckDir: EventPointer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EventPointer_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EventPointer.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘EventPointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EventPointer’ version ‘3.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘SGSeq:::addFeatureID’ ‘SGSeq:::addGeneID’ ‘SGSeq:::edges’
  ‘SGSeq:::exonGraph’ ‘SGSeq:::feature2name’ ‘SGSeq:::matchSGFeatures’
  ‘SGSeq:::nodes’ ‘SGSeq:::propagateAnnotation’
  ‘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’
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’
callGRseq_parallel: no visible global function definition for
  ‘makeCluster’
callGRseq_parallel: no visible binding for global variable ‘i’
callGRseq_parallel: no visible global function definition for
  ‘stopCluster’
call_get_table_Bootstrap: no visible global function definition for
  ‘makeCluster’
call_get_table_Bootstrap: no visible binding for global variable ‘ii’
call_get_table_Bootstrap: no visible global function definition for
  ‘stopCluster’
fitgl: no visible binding for global variable ‘hist’
myphyper: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  PSI_table addDummySpliceSites annotatePaths dhyper hist i ii jj
  makeCluster matchTxFeatures stopCluster valueRanking
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dhyper")
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 ... NOTE
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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/EventPointer.Rcheck/00check.log’
for details.


Installation output

EventPointer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL EventPointer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘EventPointer’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dgl.c -o dgl.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c params.c -o params.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c pgl.c -o pgl.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c qdgl.c -o qdgl.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c qgl.c -o qgl.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rgl.c -o rgl.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o EventPointer.so dgl.o params.o pgl.o qdgl.o qgl.o rgl.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

EventPointer.Rcheck/tests/runTests.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: '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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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...Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...1 2 3 4 


RUNIT TEST PROTOCOL -- Wed Jun 12 23:04:30 2024 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
EventPointer RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.850   0.767  14.610 

Example timings

EventPointer.Rcheck/EventPointer-Ex.timings

nameusersystemelapsed
CDFfromGTF000
CDFfromGTF_Multipath0.0010.0000.001
EventDetection000
EventDetectionMultipath000
EventDetection_transcriptome000
EventPointer0.0450.0000.045
EventPointer_Bootstraps0.1250.0030.129
EventPointer_IGV000
EventPointer_RNASeq0.060.000.06
EventPointer_RNASeq_IGV000
EventPointer_RNASeq_TranRef000
EventPointer_RNASeq_TranRef_IGV0.3530.0040.357
Events_ReClassification1.2400.0041.243
FindPrimers000
GetPSI_FromTranRef0.2200.0000.225
PSI_Statistic000
PrepareBam_EP000
Protein_Domain_Enrichment000
ResulTable0.1010.0000.100
getbootstrapdata0.2040.0080.212