| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:13 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1820/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.62.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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: 1.62.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings rtracklayer_1.62.0.tar.gz |
| StartedAt: 2023-11-02 13:57:54 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 14:11:54 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 840.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rtracklayer.Rcheck |
| Warnings: 5 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings rtracklayer_1.62.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/rtracklayer.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.62.0’
* 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:
bigBedHelper.c:148:3: warning: ‘strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
ucsc/basicBed.c:997:1: warning: ‘strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
ucsc/bigBed.c:314:2: warning: ‘%s’ directive argument is null [-Wformat-overflow=]
ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
ucsc/net.c:148:31: warning: passing argument 3 to ‘restrict’-qualified parameter aliases with argument 4 [-Wrestrict]
See ‘/home/biocbuild/bbs-3.18-bioc/meat/rtracklayer.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.8Mb
libs 2.2Mb
* 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 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 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: (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: (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 documentation object 'UCSCView-class':
Slots for class 'UCSCView'
Code: form hgsid session
Inherited: session
Docs: hgsid session
* checking Rd \usage sections ... OK
* 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 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-4.3.1/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 ‘puts’, possibly from ‘printf’ (C), ‘puts’ (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 35.314 2.599 37.979
GenomicData 0.536 0.083 14.208
* 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 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: 5 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
rtracklayer.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c readGFF.c -o readGFF.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bbiHelper.c -o bbiHelper.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bigWig.c -o bigWig.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bigBedHelper.c -o bigBedHelper.o
bigBedHelper.c: In function ‘bbNamedFileChunkKey’:
bigBedHelper.c:148:3: warning: ‘strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
148 | strncpy(keyBuf,item->name, maxBedNameSize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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:226:22: warning: ‘typeId’ may be used uninitialized in this function [-Wmaybe-uninitialized]
226 | switch(typeId[efIndex]) {
| ^
bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
236 | INTEGER(lengthIndex)[efIndex] = index + 1;
| ^~~~~~~~~~~~~~~~~~~~
bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized in this function [-Wmaybe-uninitialized]
218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:209:7: warning: ‘itemRgb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
205 | INTEGER(thickStart)[i] = bed->thickStart;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:198:7: warning: ‘score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
198 | INTEGER(score)[i] = bed->score;
| ^~~~~~~~~~~~~~
bigBed.c:257:5: warning: ‘name’ may be used uninitialized in this function [-Wmaybe-uninitialized]
257 | SET_VECTOR_ELT(ans, index++, name);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c twoBit.c -o twoBit.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c handlers.c -o handlers.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/aliType.c -o ucsc/aliType.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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:997:1: warning: ‘strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
997 | strncpy(dupe, itemRgb, sizeof(dupe));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c: In function ‘extractField’:
ucsc/bigBed.c:314:2: warning: ‘%s’ directive argument is null [-Wformat-overflow=]
314 | warn("Not enough fields in extractField of %s", line);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
In function ‘writeIndexLevel’,
inlined from ‘bptFileBulkIndexToOpenFile’ at ucsc/bPlusTree.c:567:29:
ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
461 | keyBuf[keySize] = 0;
| ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function ‘bptFileBulkIndexToOpenFile’:
ucsc/bPlusTree.c:460:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
460 | char keyBuf[keySize+1];
| ^~~~~~
In function ‘writeLeafLevel’,
inlined from ‘bptFileBulkIndexToOpenFile’ at ucsc/bPlusTree.c:575:1:
ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
513 | keyBuf[keySize] = 0;
| ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function ‘bptFileBulkIndexToOpenFile’:
ucsc/bPlusTree.c:512:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
512 | char keyBuf[keySize+1];
| ^~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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:187:18: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable]
187 | char *blockPt, *blockEnd;
| ^~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/hex.c -o ucsc/hex.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o
In file included from ucsc/udc.c:41:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
ucsc/udc.c: In function ‘djb2_hash’:
ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
1088 | while (c = *str++)
| ^
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o
In file included from ucsc/net.c:19:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
ucsc/net.c: In function ‘netConnectWithTimeout’:
ucsc/net.c:148:31: warning: passing argument 3 to ‘restrict’-qualified parameter aliases with argument 4 [-Wrestrict]
148 | res = select(sd+1, NULL, &mySet, &mySet, &tempTime);
| ^~~~~~ ~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
In file included from ucsc/twoBit.c:15:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
In file included from ucsc/https.c:17:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/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/aliType.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/hex.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 -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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("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, setdiff, sort, 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 -- Thu Nov 2 14:11:49 2023
***********************************************
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
52.972 3.208 487.484
rtracklayer.Rcheck/rtracklayer-Ex.timings
| name | user | system | elapsed | |
| BEDFile-class | 3.205 | 0.067 | 3.387 | |
| BamFile-methods | 0.122 | 0.024 | 0.148 | |
| BigBedFile | 0.352 | 0.032 | 0.385 | |
| BigBedSelection | 0.026 | 0.008 | 0.034 | |
| BigWigFile | 35.314 | 2.599 | 37.979 | |
| BigWigSelection-class | 0.025 | 0.000 | 0.025 | |
| GFFFile-class | 1.383 | 0.103 | 1.493 | |
| GenomicData | 0.536 | 0.083 | 14.208 | |
| GenomicSelection | 0.136 | 0.000 | 0.136 | |
| Quickload-class | 0.018 | 0.000 | 0.020 | |
| QuickloadGenome-class | 0.121 | 0.004 | 0.126 | |
| TrackHub-class | 0.043 | 0.007 | 0.053 | |
| TrackHubGenome-class | 0.018 | 0.000 | 0.019 | |
| TwoBitFile-class | 0.097 | 0.020 | 0.119 | |
| UCSCSchema-class | 0.000 | 0.000 | 0.001 | |
| UCSCTableQuery-class | 0 | 0 | 0 | |
| WIGFile-class | 1.111 | 0.052 | 1.168 | |
| asBED | 0 | 0 | 0 | |
| asGFF | 0 | 0 | 0 | |
| browseGenome | 0.001 | 0.000 | 0.000 | |
| browserView-methods | 0 | 0 | 0 | |
| browserViews-methods | 0 | 0 | 0 | |
| cpneTrack | 0.822 | 0.036 | 0.859 | |
| layTrack-methods | 0.001 | 0.000 | 0.000 | |
| liftOver | 0 | 0 | 0 | |
| readGFF | 0.415 | 0.000 | 0.417 | |
| targets | 0.053 | 0.000 | 0.054 | |
| ucscGenomes | 0.290 | 0.008 | 3.718 | |
| ucscTrackModes-methods | 0.017 | 0.000 | 0.016 | |