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 12:08 -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 1820/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rtracklayer 1.66.0 (landing page) Michael Lawrence
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the rtracklayer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rtracklayer.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: rtracklayer |
Version: 1.66.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rtracklayer_1.66.0.tar.gz |
StartedAt: 2024-11-20 11:56:12 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 12:04:20 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 488.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rtracklayer.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rtracklayer_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rtracklayer.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 ‘rtracklayer/DESCRIPTION’ ... OK * this is package ‘rtracklayer’ version ‘1.66.0’ * 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 ‘rtracklayer’ can be installed ... WARNING Found the following significant warnings: ucsc/basicBed.c:449:1: warning: '__builtin_strncpy' specified bound 64 equals destination size [-Wstringop-truncation] ucsc/udc.c:1070:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] ucsc/net.c:36:1: warning: control reaches end of non-void function [-Wreturn-type] ucsc/net.c:57:1: warning: control reaches end of non-void function [-Wreturn-type] ucsc/net.c:187:1: warning: control reaches end of non-void function [-Wreturn-type] ucsc/https.c:76:5: warning: 'ERR_load_SSL_strings' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] See ‘/home/biocbuild/bbs-3.20-bioc/meat/rtracklayer.Rcheck/00install.out’ for details. * 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 ... NOTE License components with restrictions not permitted: Artistic-2.0 + file LICENSE * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE ':::' call which should be '::': ‘XVector:::open_input_files’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘BiocGenerics:::testPackage’ ‘GenomicRanges:::INVALID.GR.COLNAMES’ ‘S4Vectors:::labeledLine’ ‘S4Vectors:::make_XYZxyz_to_XxYyZz_subscript’ ‘S4Vectors:::new_SimpleList_from_list’ ‘XVector:::rewind_filexp’ 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 import,BEDPEFile-ANY-ANY: no visible binding for global variable ‘chrom2’ import,BEDPEFile-ANY-ANY: no visible binding for global variable ‘start2’ import,BEDPEFile-ANY-ANY: no visible binding for global variable ‘end2’ import,BEDPEFile-ANY-ANY: no visible binding for global variable ‘strand2’ Undefined global functions or variables: chrom2 end2 start2 strand2 * checking Rd files ... WARNING checkRd: (5) BigBedFile.Rd:96-101: \item in \describe must have non-empty label checkRd: (5) BigBedSelection.rd:23-30: \item in \describe must have non-empty label checkRd: (5) BigBedSelection.rd:36-42: \item in \describe must have non-empty label checkRd: (5) BigWigFile.Rd:137-142: \item in \describe must have non-empty label checkRd: (5) BigWigFile.Rd:143-172: \item in \describe must have non-empty label checkRd: (5) BigWigSelection-class.Rd:21-29: \item in \describe must have non-empty label checkRd: (5) BigWigSelection-class.Rd:35-41: \item in \describe must have non-empty label checkRd: (5) BrowserViewList-class.Rd:19-22: \item in \describe must have non-empty label checkRd: (5) Chain-class.Rd:49-55: \item in \describe must have non-empty label checkRd: (5) Chain-class.Rd:56-59: \item in \describe must have non-empty label checkRd: (5) Chain-class.Rd:60-62: \item in \describe must have non-empty label checkRd: (5) Chain-class.Rd:63-65: \item in \describe must have non-empty label checkRd: (5) Chain-class.Rd:66-69: \item in \describe must have non-empty label checkRd: (5) Chain-class.Rd:83-88: \item in \describe must have non-empty label checkRd: (5) GFFFile-class.Rd:248-250: \item in \describe must have non-empty label checkRd: (5) GenomicData.Rd:24-28: \item in \describe must have non-empty label checkRd: (5) GenomicData.Rd:29-35: \item in \describe must have non-empty label checkRd: (5) GenomicData.Rd:41-57: \item in \describe must have non-empty label checkRd: (5) IntegerRangesList-methods.Rd:26-30: \item in \describe must have non-empty label checkRd: (5) Quickload-class.Rd:36-43: \item in \describe must have non-empty label checkRd: (5) Quickload-class.Rd:52-55: \item in \describe must have non-empty label checkRd: (5) Quickload-class.Rd:56-57: \item in \describe must have non-empty label checkRd: (5) Quickload-class.Rd:58-60: \item in \describe must have non-empty label checkRd: (5) Quickload-class.Rd:61-63: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:48-72: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:81-86: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:87-90: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:91-94: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:95-98: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:99-102: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:103-106: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:112-114: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:115-117: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:118-120: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:121-123: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:124-150: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:151-154: \item in \describe must have non-empty label checkRd: (5) QuickloadGenome-class.Rd:155-159: \item in \describe must have non-empty label checkRd: (-1) TabixFile-methods.Rd:16: Lost braces 16 | \code{Rsamtools:TabixFile}{TabixFile} objects. These are generally | ^ checkRd: (5) TrackDb-class.Rd:30-32: \item in \describe must have non-empty label checkRd: (5) TrackDb-class.Rd:33-35: \item in \describe must have non-empty label checkRd: (5) TrackDb-class.Rd:36-38: \item in \describe must have non-empty label checkRd: (5) TrackDb-class.Rd:39-42: \item in \describe must have non-empty label checkRd: (5) TrackDb-class.Rd:43-49: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:56-63: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:72-75: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:76-77: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:78-80: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:81-83: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:84-88: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:95-97: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:98-100: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:101-103: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:104-106: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:107-109: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:110-112: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:113-115: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:116-118: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:119-121: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:122-124: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:125-127: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:128-130: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:131-133: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:134-136: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:137-139: \item in \describe must have non-empty label checkRd: (5) TrackHub-class.Rd:140-144: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:45-59: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:67-70: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:71-74: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:75-77: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:78-80: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:81-83: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:84-87: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:88-91: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:92-94: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:95-97: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:98-100: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:106-108: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:109-128: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:129-132: \item in \describe must have non-empty label checkRd: (5) TrackHubGenome-class.Rd:133-137: \item in \describe must have non-empty label checkRd: (5) TwoBitFile-class.Rd:106-111: \item in \describe must have non-empty label checkRd: (5) UCSCSchema-class.Rd:25: \item in \describe must have non-empty label checkRd: (5) UCSCSchema-class.Rd:26: \item in \describe must have non-empty label checkRd: (5) UCSCSchema-class.Rd:27: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:92-102: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:110-114: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:115-122: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:123-126: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:135-137: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:138-140: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:141-145: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:146-152: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:153-156: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:157-158: \item in \describe must have non-empty label checkRd: (5) UCSCTableQuery-class.Rd:159-162: \item in \describe must have non-empty label checkRd: (-1) layTrack-methods.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) layTrack-methods.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (5) ucscSession-class.Rd:100-105: \item in \describe must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘FileForFormat’ ‘Genome’ ‘Track’ ‘TrackContainer’ ‘browserSession<-’ ‘cleanupBigBedCache’ ‘descriptionUrl’ ‘descriptionUrl<-’ ‘email’ ‘email<-’ ‘genomeField’ ‘genomeField<-’ ‘genomeInfo’ ‘genomeInfo<-’ ‘genomesFile’ ‘genomesFile<-’ ‘getTracks’ ‘hub’ ‘hub<-’ ‘hubUrl<-’ ‘longLabel’ ‘longLabel<-’ ‘readGFFAsGRanges’ ‘readGFFPragmas’ ‘shortLabel’ ‘shortLabel<-’ ‘sniffGFFVersion’ ‘trackField’ ‘trackField<-’ ‘trackName’ ‘trackName<-’ Undocumented S4 classes: ‘Track’ ‘RTLFile’ ‘TrackContainer’ ‘RTLFileList’ Undocumented S4 methods: generic 'as.character' and siglist 'RTLFile' generic 'browserSession' and siglist 'UCSCTableQuery' generic 'browserSession<-' and siglist 'UCSCTableQuery' generic 'export' and siglist 'CompressedGRangesList,BEDFile,ANY' generic 'export' and siglist 'CompressedGRangesList,GFFFile,ANY' generic 'export' and siglist 'GRangesList,UCSCFile,ANY' generic 'export' and siglist 'SimpleGRangesList,BEDFile,ANY' generic 'export' and siglist 'SimpleGRangesList,GFFFile,ANY' generic 'export' and siglist 'SimpleGRangesList,WIGFile,ANY' generic 'fileFormat' and siglist 'Bed15TrackLine' generic 'fileFormat' and siglist 'GraphTrackLine' generic 'fileFormat' and siglist 'RTLFile' generic 'fileFormat' and siglist 'TrackLine' generic 'genomesFile' and siglist 'TrackHub' generic 'genomesFile<-' and siglist 'TrackHub' generic 'initialize' and siglist 'RTLFile' generic 'liftOver' and siglist 'GRangesList,Chain' generic 'names' and siglist 'GenomeContainer' generic 'names' and siglist 'Quickload' generic 'names' and siglist 'TrackContainer' generic 'names' and siglist 'TrackHub' generic 'path' and siglist 'RTLFile' generic 'show' and siglist 'RTLFile' generic 'show' and siglist 'UCSCSchema' generic 'track<-' and siglist 'TrackHubGenome,BiocFile' generic 'track<-' and siglist 'UCSCSession,SimpleGRangesList' generic 'trackName' and siglist 'UCSCTableQuery' generic 'trackName<-' and siglist 'UCSCTableQuery' generic 'trackNames' and siglist 'QuickloadGenome' generic 'trackNames' and siglist 'TrackHubGenome' generic 'trackNames' and siglist 'UCSCTableQuery' generic 'uri' and siglist 'Quickload' generic 'uri' and siglist 'TrackHub' generic 'writeTrackHub' and siglist 'TrackHub' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING S4 class codoc mismatches from Rd file 'ucscView-class.Rd': Slots for class 'UCSCView' Code: form hgsid session Inherited: session Docs: hgsid session * checking Rd \usage sections ... OK * checking Rd contents ... NOTE Argument items with no description in Rd file 'readGFF.Rd': ‘filter’ ‘raw_data’ ‘GFF1’ * 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 shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/R/R-4.4.1/site-library/rtracklayer/libs/rtracklayer.so’: Found ‘_exit’, possibly from ‘_exit’ (C) Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘printf’, possibly from ‘printf’ (C) Found ‘rand’, possibly from ‘rand’ (C) Found ‘sprintf’, possibly from ‘sprintf’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (C) File ‘rtracklayer/libs/rtracklayer.so’: Found non-API calls to R: ‘R_ReadConnection’, ‘R_ignore_SIGPIPE’, ‘getConnection’ 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 nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. Compiled code should not call non-API entry points in R. 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 BigWigFile 36.180 1.194 37.430 GenomicData 0.498 0.095 10.288 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘rtracklayer_unit_tests.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: 5 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/rtracklayer.Rcheck/00check.log’ for details.
rtracklayer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL rtracklayer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘rtracklayer’ ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... yes configure: creating ./config.status config.status: creating src/Makevars ** 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 -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c readGFF.c -o readGFF.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bbiHelper.c -o bbiHelper.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bigWig.c -o bigWig.o bigWig.c: In function 'BWGFile_query': bigWig.c:268:11: warning: 'ans_nhits' may be used uninitialized [-Wmaybe-uninitialized] 268 | INTEGER(ans_nhits)[i] = nqhits; | ^~~~~~~~~~~~~~~~~~ bigWig.c:231:58: note: 'ans_nhits' was declared here 231 | SEXP ans, ans_start, ans_width, ans_score, ans_ranges, ans_nhits; | ^~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bigBedHelper.c -o bigBedHelper.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bigBed.c -o bigBed.o bigBed.c: In function 'BBDFile_write': bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable] 338 | bits64 extraIndexListEndOffset = 0; | ^~~~~~~~~~~~~~~~~~~~~~~ bigBed.c: In function 'BBDFile_query': bigBed.c:195:7: warning: 'name' may be used uninitialized [-Wmaybe-uninitialized] 195 | SET_STRING_ELT(name, i, mkChar(bed->name)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:74:54: note: 'name' was declared here 74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score, | ^~~~ bigBed.c:198:7: warning: 'score' may be used uninitialized [-Wmaybe-uninitialized] 198 | INTEGER(score)[i] = bed->score; | ^~~~~~~~~~~~~~ bigBed.c:74:60: note: 'score' was declared here 74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score, | ^~~~~ bigBed.c:205:7: warning: 'thickStart' may be used uninitialized [-Wmaybe-uninitialized] 205 | INTEGER(thickStart)[i] = bed->thickStart; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:75:26: note: 'thickStart' was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~~~~~ bigBed.c:204:7: warning: 'thickWidth' may be used uninitialized [-Wmaybe-uninitialized] 204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:75:38: note: 'thickWidth' was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~~~~~ bigBed.c:209:7: warning: 'itemRgb' may be used uninitialized [-Wmaybe-uninitialized] 209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:75:50: note: 'itemRgb' was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~~ bigBed.c:218:7: warning: 'blocks' may be used uninitialized [-Wmaybe-uninitialized] 218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:75:59: note: 'blocks' was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~ bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized [-Wmaybe-uninitialized] 236 | INTEGER(lengthIndex)[efIndex] = index + 1; | ^~~~~~~~~~~~~~~~~~~~ bigBed.c:76:31: note: 'lengthIndex' was declared here 76 | extraFields = R_NilValue, lengthIndex; | ^~~~~~~~~~~ bigBed.c:226:22: warning: 'typeId' may be used uninitialized [-Wmaybe-uninitialized] 226 | switch(typeId[efIndex]) { | ^ bigBed.c:141:13: note: 'typeId' was declared here 141 | SEXPTYPE *typeId; | ^~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chain_io.c -o chain_io.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c twoBit.c -o twoBit.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c handlers.c -o handlers.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/memgfx.c -o ucsc/memgfx.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/binRange.c -o ucsc/binRange.o ucsc/binRange.c:49:12: warning: 'binFromRangeExtended' defined but not used [-Wunused-function] 49 | static int binFromRangeExtended(int start, int end) | ^~~~~~~~~~~~~~~~~~~~ ucsc/binRange.c:28:12: warning: 'binFromRangeStandard' defined but not used [-Wunused-function] 28 | static int binFromRangeStandard(int start, int end) | ^~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/htmlColor.c -o ucsc/htmlColor.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/tokenizer.c -o ucsc/tokenizer.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/asParse.c -o ucsc/asParse.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/basicBed.c -o ucsc/basicBed.o ucsc/basicBed.c: In function 'bedParseRgb': ucsc/basicBed.c:449:1: warning: '__builtin_strncpy' specified bound 64 equals destination size [-Wstringop-truncation] 449 | strncpy(dupe, itemRgb, sizeof(dupe)); | ^~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bigBed.c -o ucsc/bigBed.o ucsc/bigBed.c:326:31: warning: 'bigBedIntervalsMatchingName' defined but not used [-Wunused-function] 326 | static struct bigBedInterval *bigBedIntervalsMatchingName(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/bigBed.c:311:16: warning: 'bbWordIsInHash' defined but not used [-Wunused-function] 311 | static boolean bbWordIsInHash(char *line, int fieldIx, void *target) | ^~~~~~~~~~~~~~ ucsc/bigBed.c:301:16: warning: 'bbWordMatchesName' defined but not used [-Wunused-function] 301 | static boolean bbWordMatchesName(char *line, int fieldIx, void *target) | ^~~~~~~~~~~~~~~~~ ucsc/bigBed.c:252:31: warning: 'bigBedChunksMatchingNames' defined but not used [-Wunused-function] 252 | static struct fileOffsetSize *bigBedChunksMatchingNames(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/bigBed.c:241:31: warning: 'bigBedChunksMatchingName' defined but not used [-Wunused-function] 241 | static struct fileOffsetSize *bigBedChunksMatchingName(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~~ ucsc/bigBed.c:150:28: warning: 'bigBedCoverageIntervals' defined but not used [-Wunused-function] 150 | static struct bbiInterval *bigBedCoverageIntervals(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o ucsc/bwgQuery.c: In function 'bigWigIntervalQuery': ucsc/bwgQuery.c:164:25: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable] 164 | char *blockPt, *blockEnd; | ^~~~~~~~ ucsc/bwgQuery.c: At top level: ucsc/bwgQuery.c:47:12: warning: 'bigWigBlockDumpIntersectingRange' defined but not used [-Wunused-function] 47 | static int bigWigBlockDumpIntersectingRange(boolean isSwapped, char *blockPt, char *blockEnd, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o ucsc/cirTree.c:530:13: warning: 'rEnumerateBlocks' defined but not used [-Wunused-function] 530 | static void rEnumerateBlocks(struct cirTreeFile *crt, int level, bits64 indexFileOffset, | ^~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o ucsc/common.c:1971:13: warning: 'dateAdd' defined but not used [-Wunused-function] 1971 | static void dateAdd(struct tm *tp,int addYears,int addMonths,int addDays) | ^~~~~~~ ucsc/common.c:1901:14: warning: 'emptyStr' defined but not used [-Wunused-variable] 1901 | static char *emptyStr = ""; | ^~~~~~~~ ucsc/common.c:1900:14: warning: 'naStr' defined but not used [-Wunused-variable] 1900 | static char *naStr = "n/a"; | ^~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o ucsc/dnautil.c:521:12: warning: 'findHeadPolyTMaybeMask' defined but not used [-Wunused-function] 521 | static int findHeadPolyTMaybeMask(DNA *dna, int size, boolean doMask, | ^~~~~~~~~~~~~~~~~~~~~~ ucsc/dnautil.c:465:12: warning: 'findTailPolyAMaybeMask' defined but not used [-Wunused-function] 465 | static int findTailPolyAMaybeMask(DNA *dna, int size, boolean doMask, | ^~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o ucsc/errAbort.c:218:13: warning: 'warnAbortHandler' defined but not used [-Wunused-function] 218 | static void warnAbortHandler(char *format, va_list args) | ^~~~~~~~~~~~~~~~ ucsc/errAbort.c:210:13: warning: 'debugAbort' defined but not used [-Wunused-function] 210 | static void debugAbort() | ^~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o ucsc/obscure.c:14:12: warning: '_dotForUserMod' defined but not used [-Wunused-variable] 14 | static int _dotForUserMod = 100; /* How often does dotForUser() output a dot. */ | ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o ucsc/rangeTree.c:36:14: warning: 'sumInt' defined but not used [-Wunused-function] 36 | static void *sumInt(void *a, void *b) | ^~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o ucsc/rbTree.c:680:13: warning: 'addRefWithContext' defined but not used [-Wunused-function] 680 | static void addRefWithContext(void *item, void *context) | ^~~~~~~~~~~~~~~~~ ucsc/rbTree.c:674:13: warning: 'addRef' defined but not used [-Wunused-function] 674 | static void addRef(void *item) | ^~~~~~ ucsc/rbTree.c:576:13: warning: 'rTreeDump' defined but not used [-Wunused-function] 576 | static void rTreeDump(struct rbTreeNode *n) | ^~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o ucsc/memalloc.c:357:14: warning: 'memTrackerRealloc' defined but not used [-Wunused-function] 357 | static void *memTrackerRealloc(void *vpt, size_t size) | ^~~~~~~~~~~~~~~~~ ucsc/memalloc.c:348:13: warning: 'memTrackerFree' defined but not used [-Wunused-function] 348 | static void memTrackerFree(void *vpt) | ^~~~~~~~~~~~~~ ucsc/memalloc.c:314:26: warning: 'carefulMemHandler' defined but not used [-Wunused-variable] 314 | static struct memHandler carefulMemHandler = | ^~~~~~~~~~~~~~~~~ ucsc/memalloc.c:220:13: warning: 'carefulMemInit' defined but not used [-Wunused-function] 220 | static void carefulMemInit(size_t maxToAlloc) | ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o ucsc/dlist.c:124:12: warning: 'dlNodeCmp' defined but not used [-Wunused-function] 124 | static int dlNodeCmp(const void *elem1, const void *elem2) | ^~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/filePath.c -o ucsc/filePath.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/htmlPage.c -o ucsc/htmlPage.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o ucsc/udc.c: In function 'djb2_hash': ucsc/udc.c:1070:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1070 | while (c = *str++) | ^ ucsc/udc.c: At top level: ucsc/udc.c:1273:13: warning: 'qDecode' defined but not used [-Wunused-function] 1273 | static void qDecode(const char *input, char *buf, size_t size) | ^~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o ucsc/net.c: In function 'netUrlOpenSockets': ucsc/net.c:168:22: warning: unused variable 'status' [-Wunused-variable] 168 | CURLcode status = wrapped_curl_request(curl, GET); | ^~~~~~ ucsc/net.c: In function 'header_get_last_modified': ucsc/net.c:36:1: warning: control reaches end of non-void function [-Wreturn-type] 36 | } | ^ ucsc/net.c: In function 'header_get_content_length': ucsc/net.c:57:1: warning: control reaches end of non-void function [-Wreturn-type] 57 | } | ^ ucsc/net.c: In function 'netUrlOpenSockets': ucsc/net.c:187:1: warning: control reaches end of non-void function [-Wreturn-type] 187 | } | ^ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o ucsc/https.c: In function 'openSslInit': ucsc/https.c:76:5: warning: 'ERR_load_SSL_strings' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] 76 | ERR_load_SSL_strings(); | ^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/miniforge3/include/openssl/sslerr.h:17, from /home/biocbuild/miniforge3/include/openssl/ssl.h:44, from ucsc/https.c:8: /home/biocbuild/miniforge3/include/openssl/sslerr_legacy.h:29:27: note: declared here 29 | OSSL_DEPRECATEDIN_3_0 int ERR_load_SSL_strings(void); | ^~~~~~~~~~~~~~~~~~~~ ucsc/https.c: At top level: ucsc/https.c:27:13: warning: 'openssl_locking_callback' defined but not used [-Wunused-function] 27 | static void openssl_locking_callback(int mode, int n, const char * file, int line) | ^~~~~~~~~~~~~~~~~~~~~~~~ ucsc/https.c:22:22: warning: 'openssl_id_callback' defined but not used [-Wunused-function] 22 | static unsigned long openssl_id_callback(void) | ^~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -lssl -lcrypto -lcurl -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-rtracklayer/00new/rtracklayer/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’ ** 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 (rtracklayer)
rtracklayer.Rcheck/tests/rtracklayer_unit_tests.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. > require("rtracklayer") || stop("unable to load rtracklayer package") Loading required package: rtracklayer 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, 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb [1] TRUE > rtracklayer:::.test() Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'BiocIO' The following object is masked from 'package:rtracklayer': FileForFormat Warning in readGFF(filepath, version = version, filter = filter) : connection is not positioned at the start of the file, rewinding it Warning in readGFF(filepath, version = version, filter = filter) : connection is not positioned at the start of the file, rewinding it Warning in readGFF(filepath, version = version, filter = filter) : connection is not positioned at the start of the file, rewinding it For efficiency, consider converting this WIG file to a BigWig file; see ?wigToBigWig RUNIT TEST PROTOCOL -- Wed Nov 20 12:04:14 2024 *********************************************** Number of test functions: 11 Number of errors: 0 Number of failures: 0 1 Test Suite : rtracklayer RUnit Tests - 11 test functions, 0 errors, 0 failures Number of test functions: 11 Number of errors: 0 Number of failures: 0 There were 16 warnings (use warnings() to see them) > > proc.time() user system elapsed 54.678 1.811 138.815
rtracklayer.Rcheck/rtracklayer-Ex.timings
name | user | system | elapsed | |
BEDFile-class | 2.315 | 0.103 | 2.423 | |
BamFile-methods | 1.070 | 0.040 | 1.112 | |
BigBedFile | 0.350 | 0.000 | 0.351 | |
BigBedSelection | 0.031 | 0.000 | 0.031 | |
BigWigFile | 36.180 | 1.194 | 37.430 | |
BigWigSelection-class | 0.020 | 0.004 | 0.025 | |
GFFFile-class | 1.342 | 0.052 | 1.396 | |
GenomicData | 0.498 | 0.095 | 10.288 | |
GenomicSelection | 0.126 | 0.004 | 0.130 | |
Quickload-class | 0.015 | 0.004 | 0.021 | |
QuickloadGenome-class | 0.108 | 0.020 | 0.129 | |
TrackHub-class | 0.053 | 0.000 | 0.054 | |
TrackHubGenome-class | 0.013 | 0.007 | 0.019 | |
TwoBitFile-class | 0.101 | 0.012 | 0.113 | |
UCSCSchema-class | 0 | 0 | 0 | |
UCSCTableQuery-class | 0 | 0 | 0 | |
WIGFile-class | 1.090 | 0.096 | 1.189 | |
asBED | 0 | 0 | 0 | |
asGFF | 0 | 0 | 0 | |
browseGenome | 0 | 0 | 0 | |
browserView-methods | 0 | 0 | 0 | |
browserViews-methods | 0 | 0 | 0 | |
cpneTrack | 0.834 | 0.016 | 0.850 | |
layTrack-methods | 0 | 0 | 0 | |
liftOver | 0 | 0 | 0 | |
readGFF | 0.407 | 0.032 | 0.440 | |
targets | 0.056 | 0.000 | 0.056 | |
ucscGenomes | 0.262 | 0.032 | 2.465 | |
ucscTrackModes-methods | 0.016 | 0.004 | 0.021 | |