Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:35:25 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 896/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GSReg 1.34.0 (landing page) Bahman Afsari
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
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. |
Package: GSReg |
Version: 1.34.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GSReg.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GSReg_1.34.0.tar.gz |
StartedAt: 2023-10-15 21:53:14 -0400 (Sun, 15 Oct 2023) |
EndedAt: 2023-10-15 21:57:30 -0400 (Sun, 15 Oct 2023) |
EllapsedTime: 256.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GSReg.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GSReg.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GSReg_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GSReg.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘GSReg/DESCRIPTION’ ... OK * this is package ‘GSReg’ version ‘1.34.0’ * 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 ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * used C++ compiler: ‘g++ (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 R 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING 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 Codoc mismatches from documentation object 'GSReg.GeneSets.DIRAC': 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 documentation object 'GSReg.GeneSets.EVA': 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 * checking Rd \usage sections ... WARNING Objects in \usage without \alias in documentation object 'GSReg.kendall.tau.distance': ‘GSReg.kendall.tau.distance.template’ Bad \usage lines found in documentation object 'GSReg.overlapJunction': 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 documentation object 'GSReg.SEVA': 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GSReg.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GSReg.Rcheck/00check.log’ for details.
GSReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GSReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘GSReg’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c kendallTauDistance.cc -o kendallTauDistance.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nij.cc -o nij.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vect2compC.cc -o vect2compC.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o GSReg.so init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-GSReg/00new/GSReg/libs ** R ** data ** 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 (GSReg)
GSReg.Rcheck/GSReg-Ex.timings
name | user | system | elapsed | |
GSReg_GeneSets_DIRAC | 2.308 | 0.204 | 2.709 | |
GSReg_GeneSets_VReg. | 2.181 | 0.064 | 3.733 | |
GSReg_Kendall | 0.008 | 0.000 | 0.008 | |
GSReg_OverlapJunction | 3.763 | 0.160 | 4.159 | |
GSReg_SEVA | 3.609 | 0.218 | 4.219 | |