Michael Lawrence
| Snapshot Date: 2025-05-12 13:40 -0400 (Mon, 12 May 2025) |
| git_url: https://git.bioconductor.org/packages/rtracklayer |
| git_branch: RELEASE_3_21 |
| git_last_commit: aa5ace3 |
| git_last_commit_date: 2025-04-15 09:41:54 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-05-15 11:46 -0400 (Thu, 15 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4833 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4575 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4600 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4554 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4571 |
| 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 1852/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.68.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: rtracklayer |
| Version: 1.68.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rtracklayer_1.68.0.tar.gz |
| StartedAt: 2025-05-14 07:33:00 -0400 (Wed, 14 May 2025) |
| EndedAt: 2025-05-14 07:39:07 -0400 (Wed, 14 May 2025) |
| EllapsedTime: 366.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rtracklayer.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rtracklayer_1.68.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rtracklayer.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88129)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.68.0’
* 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 ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
installed size is 8.5Mb
sub-directories of 1Mb or more:
R 2.1Mb
libs 5.0Mb
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
GRangesForUCSCGenome.Rd: genome
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘Genome’ ‘Track’ ‘TrackContainer’ ‘cleanupBigBedCache’
‘descriptionUrl’ ‘descriptionUrl<-’ ‘email’ ‘email<-’ ‘genomeField’
‘genomeField<-’ ‘genomeInfo’ ‘genomeInfo<-’ ‘genomesFile’
‘genomesFile<-’ ‘getTracks’ ‘hub’ ‘hub<-’ ‘hubUrl<-’ ‘longLabel’
‘longLabel<-’ ‘readGFFAsGRanges’ ‘readGFFPragmas’ ‘shortLabel’
‘shortLabel<-’ ‘sniffGFFVersion’ ‘trackField’ ‘trackField<-’
Undocumented S4 classes:
‘Track’ ‘TrackContainer’
Undocumented S4 methods:
generic 'genomesFile' and siglist 'TrackHub'
generic 'genomesFile<-' and siglist 'TrackHub'
generic 'names' and siglist 'GenomeContainer'
generic 'names' and siglist 'TrackContainer'
generic 'names' and siglist 'TrackHub'
generic 'track<-' and siglist 'TrackHubGenome,BiocFile'
generic 'trackNames' and siglist 'TrackHubGenome'
generic 'trackNames' and siglist 'UCSCTableQuery'
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 ... OK
* 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 ... OK
* 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 ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rtracklayer/libs/rtracklayer.so’:
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_sprintf’, possibly from ‘sprintf’ (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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BigWigFile 27.568 2.534 30.117
* 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: 2 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
rtracklayer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rtracklayer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘rtracklayer’ ... ** this is package ‘rtracklayer’ version ‘1.68.0’ ** using staged installation checking for pkg-config... /opt/R/arm64/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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readGFF.c -o readGFF.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bbiHelper.c -o bbiHelper.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bigWig.c -o bigWig.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bigBedHelper.c -o bigBedHelper.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bigBed.c -o bigBed.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chain_io.c -o chain_io.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c twoBit.c -o twoBit.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c handlers.c -o handlers.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/memgfx.c -o ucsc/memgfx.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/htmlColor.c -o ucsc/htmlColor.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/sqlList.c -o ucsc/sqlList.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/tokenizer.c -o ucsc/tokenizer.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/asParse.c -o ucsc/asParse.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/basicBed.c -o ucsc/basicBed.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bigBed.c -o ucsc/bigBed.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/errAbort.c -o ucsc/errAbort.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/hash.c -o ucsc/hash.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/filePath.c -o ucsc/filePath.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/htmlPage.c -o ucsc/htmlPage.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/udc.c -o ucsc/udc.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/net.c -o ucsc/net.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/internet.c -o ucsc/internet.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/https.c -o ucsc/https.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/os.c -o ucsc/os.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/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 /opt/R/arm64/lib/libssl.a /opt/R/arm64/lib/libcrypto.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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.
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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
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 May 14 07:38:53 2025
***********************************************
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 23 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
44.464 2.921 74.766
rtracklayer.Rcheck/rtracklayer-Ex.timings
| name | user | system | elapsed | |
| BEDFile-class | 4.186 | 0.713 | 4.911 | |
| BamFile-methods | 0.120 | 0.007 | 0.129 | |
| BigBedFile | 0.259 | 0.028 | 0.288 | |
| BigBedSelection | 0.025 | 0.003 | 0.027 | |
| BigWigFile | 27.568 | 2.534 | 30.117 | |
| BigWigSelection-class | 0.018 | 0.001 | 0.019 | |
| GFFFile-class | 1.082 | 0.118 | 1.240 | |
| GenomicData | 0.185 | 0.010 | 0.196 | |
| GenomicSelection | 0.208 | 0.009 | 0.217 | |
| Quickload-class | 0.175 | 0.017 | 0.512 | |
| QuickloadGenome-class | 0.197 | 0.009 | 0.207 | |
| TrackHub-class | 0.041 | 0.003 | 0.044 | |
| TrackHubGenome-class | 0.014 | 0.002 | 0.016 | |
| TwoBitFile-class | 0.078 | 0.004 | 0.094 | |
| UCSCSchema-class | 0 | 0 | 0 | |
| UCSCTableQuery-class | 0.000 | 0.001 | 0.001 | |
| WIGFile-class | 0.872 | 0.028 | 0.904 | |
| asBED | 0.000 | 0.000 | 0.001 | |
| asGFF | 0.000 | 0.000 | 0.001 | |
| browseGenome | 0.001 | 0.000 | 0.001 | |
| browserView-methods | 0 | 0 | 0 | |
| browserViews-methods | 0.000 | 0.001 | 0.000 | |
| cpneTrack | 0.895 | 0.065 | 1.009 | |
| layTrack-methods | 0 | 0 | 0 | |
| liftOver | 0 | 0 | 0 | |
| readGFF | 0.306 | 0.010 | 0.316 | |
| targets | 0.061 | 0.004 | 0.065 | |
| ucscGenomes | 0.191 | 0.011 | 1.127 | |
| ucscTrackModes-methods | 0.025 | 0.001 | 0.026 | |