Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 913/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GSReg 1.41.0 (landing page) Bahman Afsari
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the GSReg package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSReg.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: GSReg |
Version: 1.41.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GSReg.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GSReg_1.41.0.tar.gz |
StartedAt: 2024-12-24 07:27:28 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:30:52 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 203.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GSReg.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GSReg.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GSReg_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GSReg.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GSReg/DESCRIPTION’ ... OK * this is package ‘GSReg’ version ‘1.41.0’ * 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 ‘GSReg’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/GSReg.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 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 Packages in Depends field not imported from: ‘AnnotationDbi’ ‘GenomicFeatures’ ‘Homo.sapiens’ ‘org.Hs.eg.db’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GSReg.DIRAC.Pathways: no visible global function definition for ‘pnorm’ GSReg.DIRAC.mu: no visible global function definition for ‘var’ GSReg.Variance: no visible global function definition for ‘var’ GSReg.Variance: no visible global function definition for ‘pnorm’ GSReg.kendall.tau.distance.Restricted.Sparse.internal: no visible global function definition for ‘as’ GSReg.overlapJunction: no visible binding for global variable ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ GSReg.overlapJunction: no visible binding for global variable ‘org.Hs.eg.db’ GSReg.overlapJunction: no visible global function definition for ‘genes’ GSReg.overlapJunction: no visible global function definition for ‘mapIds’ GSReg.overlapJunction: no visible global function definition for ‘GRanges’ GSReg.overlapJunction: no visible global function definition for ‘Rle’ GSReg.overlapJunction: no visible global function definition for ‘IRanges’ GSReg.overlapJunction: no visible global function definition for ‘findOverlaps’ GSReg.overlapJunction: no visible global function definition for ‘queryHits’ GSReg.overlapJunction: no visible global function definition for ‘subjectHits’ GSReg.overlapJunction : <anonymous>: no visible global function definition for ‘findOverlaps’ GSReg.overlapJunction : <anonymous>: no visible global function definition for ‘Matrix’ GSReg.overlapJunction : <anonymous>: no visible global function definition for ‘queryHits’ GSReg.overlapJunction : <anonymous>: no visible global function definition for ‘subjectHits’ Undefined global functions or variables: GRanges IRanges Matrix Rle TxDb.Hsapiens.UCSC.hg19.knownGene as findOverlaps genes mapIds org.Hs.eg.db pnorm queryHits subjectHits var Consider adding importFrom("methods", "as") importFrom("stats", "pnorm", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) GSReg-package.Rd:20: Lost braces; missing escapes or markup? 20 | {B) Calculate the DIRAC measure and p-value for it based on permutation test;} | ^ checkRd: (-1) GSReg-package.Rd:22: Lost braces; missing escapes or markup? 22 | {C) Calculate for a modified DIRAC method and a fast-efficient p-valuebased on U-Statistic theory;} | ^ checkRd: (-1) GSReg-package.Rd:24: Lost braces; missing escapes or markup? 24 | {D) Alternative Splicing Events in genes from a phenotype to other phenotype using their junction expression;} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 Undocumented code objects: ‘GSReg.kendall.tau.distance.template’ Undocumented data sets: ‘geneExrsGSReg’ ‘junc.RPM.Simulated’ ‘phenotypes’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Codoc mismatches from Rd file 'GSReg_GeneSets_DIRAC.Rd': GSReg.GeneSets.DIRAC Code: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha = 0, minGeneNum = 5) Docs: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha = 0.05, minGeneNum = 5) Mismatches in argument default values: Name: 'alpha' Code: 0 Docs: 0.05 Codoc mismatches from Rd file 'GSReg_GeneSets_VReg..Rd': GSReg.GeneSets.EVA Code: function(geneexpres, pathways, phenotypes, verbose = T, minGeneNum = 5, distFunc = GSReg.kendall.tau.distance, distparamPathways, ...) Docs: function(geneexpres, pathways, phenotypes, minGeneNum = 5) Argument names in code not in docs: verbose distFunc distparamPathways ... Mismatches in argument names: Position: 4 Code: verbose Docs: minGeneNum Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... WARNING Objects in \usage without \alias in Rd file 'GSReg_Kendall.Rd': ‘GSReg.kendall.tau.distance.template’ Bad \usage lines found in Rd file 'GSReg_OverlapJunction.Rd': GSReg.overlapJunction <- function(juncExprs, GenestoStudy=NULL, geneexpr=NULL, minmeanloggeneexp= 3, alpha =0, sparse = F, genesCoordinatesTxDB = TxDb.Hsapiens.UCSC.hg19.knownGene, geneIDInTxDB = 'ENTREZID', geneIDOut = 'SYMBOL', org=org.Hs.eg.db, ...) Bad \usage lines found in Rd file 'GSReg_SEVA.Rd': function(juncExprs, phenoVect, verbose=T, sparse =F, ...) 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. * 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’ ... NOTE The following files look like leftovers/mistakes: ‘Rplots.pdf’ Please remove them from your package. * checking examples ... 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 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GSReg.Rcheck/00check.log’ for details.
GSReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GSReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GSReg’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init.c -o init.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c kendallTauDistance.cc -o kendallTauDistance.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c nij.cc -o nij.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c vect2compC.cc -o vect2compC.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o GSReg.so init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-GSReg/00new/GSReg/libs ** R ** data ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (GSReg)
GSReg.Rcheck/GSReg-Ex.timings
name | user | system | elapsed | |
GSReg_GeneSets_DIRAC | 2.230 | 0.048 | 2.288 | |
GSReg_GeneSets_VReg. | 1.552 | 0.004 | 1.559 | |
GSReg_Kendall | 0.003 | 0.000 | 0.004 | |
GSReg_OverlapJunction | 2.592 | 0.068 | 2.667 | |
GSReg_SEVA | 3.444 | 0.067 | 3.520 | |