Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 681/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EventPointer 3.14.0 (landing page) Juan A. Ferrer-Bonsoms
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: EventPointer |
Version: 3.14.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EventPointer_3.14.0.tar.gz |
StartedAt: 2024-11-20 07:44:50 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 07:52:14 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 443.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EventPointer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EventPointer_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EventPointer.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EventPointer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EventPointer’ version ‘3.14.0’ * 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 (conda-forge gcc 14.2.0-1) 14.2.0’ * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/EventPointer.Rcheck/00check.log’ for details.
EventPointer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL EventPointer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘EventPointer’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c dgl.c -o dgl.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c params.c -o params.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pgl.c -o pgl.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c qdgl.c -o qdgl.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c qgl.c -o qgl.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c rgl.c -o rgl.o gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o EventPointer.so dgl.o params.o pgl.o qdgl.o qgl.o rgl.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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)
EventPointer.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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, saveRDS, 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 Nov 20 07:52:11 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 18.791 0.839 19.613
EventPointer.Rcheck/EventPointer-Ex.timings
name | user | system | elapsed | |
CDFfromGTF | 0 | 0 | 0 | |
CDFfromGTF_Multipath | 0 | 0 | 0 | |
EventDetection | 0 | 0 | 0 | |
EventDetectionMultipath | 0.000 | 0.000 | 0.001 | |
EventDetection_transcriptome | 0 | 0 | 0 | |
EventPointer | 0.052 | 0.006 | 0.059 | |
EventPointer_Bootstraps | 0.191 | 0.000 | 0.194 | |
EventPointer_IGV | 0.000 | 0.000 | 0.001 | |
EventPointer_RNASeq | 0.261 | 0.000 | 0.262 | |
EventPointer_RNASeq_IGV | 0 | 0 | 0 | |
EventPointer_RNASeq_TranRef | 0 | 0 | 0 | |
EventPointer_RNASeq_TranRef_IGV | 0.321 | 0.012 | 0.334 | |
Events_ReClassification | 1.681 | 0.028 | 1.714 | |
FindPrimers | 0.001 | 0.000 | 0.000 | |
GetPSI_FromTranRef | 0.369 | 0.000 | 0.378 | |
PSI_Statistic | 0 | 0 | 0 | |
PrepareBam_EP | 0.000 | 0.000 | 0.001 | |
Protein_Domain_Enrichment | 0 | 0 | 0 | |
ResulTable | 0.227 | 0.000 | 0.227 | |
getbootstrapdata | 0.327 | 0.044 | 0.372 | |