Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:37 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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 |
To the developers/maintainers of the GenomicRanges package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicRanges.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 758/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicRanges 1.47.6 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: GenomicRanges |
Version: 1.47.6 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicRanges.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicRanges_1.47.6.tar.gz |
StartedAt: 2022-03-17 19:11:16 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 19:15:11 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 235.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicRanges.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicRanges.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicRanges_1.47.6.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GenomicRanges.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GenomicRanges/DESCRIPTION' ... OK * this is package 'GenomicRanges' version '1.47.6' * 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 whether package 'GenomicRanges' can be installed ... OK * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'D:/biocbuild/bbs-3.15-bioc/R/library/GenomicRanges/libs/x64/GenomicRanges.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genomicvars 38.45 20.14 58.59 GPos-class 27.46 7.61 35.09 makeGRangesFromDataFrame 0.53 0.05 11.08 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'run_unitTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/GenomicRanges.Rcheck/00check.log' for details.
GenomicRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GenomicRanges ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'GenomicRanges' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c transcript_utils.c -o transcript_utils.o transcript_utils.c: In function 'tlocs2rlocs': transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized] return on_minus_strand ? end - tloc : start + tloc; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c:120:24: note: 'end' was declared here int nexons, j, start, end, width; ^~~ transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized] return on_minus_strand ? end - tloc : start + tloc; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c:120:17: note: 'start' was declared here int nexons, j, start, end, width; ^~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GenomicRanges' finding HTML links ... done DelegatingGenomicRanges-class html GNCList-class html GPos-class html finding level-2 HTML links ... done GRanges-class html GRangesFactor-class html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/help/coerce+2CFactor+2CGRanges-method.html GRangesList-class html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/help/coerce+2CList+2CSimpleGRangesList-method.html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/help/coerce+2CList+2CCompressedGRangesList-method.html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/help/coerce+2CList+2CGRangesList-method.html GenomicRanges-comparison html GenomicRangesList-class html absoluteRanges html constraint html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/help/constraint.html coverage-methods html findOverlaps-methods html genomic-range-squeezers html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/help/granges.html genomicvars html inter-range-methods html intra-range-methods html makeGRangesFromDataFrame html makeGRangesListFromDataFrame html nearest-methods html phicoef html setops-methods html strand-utils html subtract-methods html tile-methods html tileGenome html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicRanges) Making 'packages.html' ... done
GenomicRanges.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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. > require("GenomicRanges") || stop("unable to load GenomicRanges package") Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb [1] TRUE > GenomicRanges:::.test() RUNIT TEST PROTOCOL -- Thu Mar 17 19:14:59 2022 *********************************************** Number of test functions: 73 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicRanges RUnit Tests - 73 test functions, 0 errors, 0 failures Number of test functions: 73 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 39.29 0.20 39.48
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
name | user | system | elapsed | |
GNCList-class | 0.29 | 0.05 | 0.34 | |
GPos-class | 27.46 | 7.61 | 35.09 | |
GRanges-class | 0.91 | 0.16 | 1.07 | |
GRangesFactor-class | 0.36 | 0.00 | 0.36 | |
GRangesList-class | 0.51 | 0.00 | 0.51 | |
GenomicRanges-comparison | 0.21 | 0.00 | 0.21 | |
absoluteRanges | 0.97 | 0.07 | 1.05 | |
constraint | 0.70 | 0.02 | 0.75 | |
coverage-methods | 0.19 | 0.00 | 0.19 | |
findOverlaps-methods | 0.84 | 0.00 | 0.84 | |
genomic-range-squeezers | 0 | 0 | 0 | |
genomicvars | 38.45 | 20.14 | 58.59 | |
inter-range-methods | 1.63 | 0.50 | 2.13 | |
intra-range-methods | 0.37 | 0.00 | 0.37 | |
makeGRangesFromDataFrame | 0.53 | 0.05 | 11.08 | |
makeGRangesListFromDataFrame | 0.08 | 0.00 | 0.08 | |
nearest-methods | 1.08 | 0.00 | 1.08 | |
phicoef | 0 | 0 | 0 | |
setops-methods | 2.20 | 0.01 | 2.22 | |
strand-utils | 0.07 | 0.00 | 0.06 | |
subtract-methods | 0.18 | 0.00 | 0.19 | |
tile-methods | 0.07 | 0.00 | 0.06 | |
tileGenome | 0.18 | 0.02 | 0.20 | |