Michael Lawrence
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/rtracklayer |
| git_branch: RELEASE_3_20 |
| git_last_commit: d81035b |
| git_last_commit_date: 2024-10-29 09:29:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1820/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.66.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 1.66.0 |
| 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_1.66.0.tar.gz |
| StartedAt: 2024-12-20 08:55:45 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 09:06:28 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 643.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rtracklayer.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.66.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rtracklayer.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.66.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rtracklayer’ can be installed ... WARNING
Found the following significant warnings:
ucsc/cirTree.c:530:13: warning: function 'rEnumerateBlocks' is not needed and will not be emitted [-Wunneeded-internal-declaration]
ucsc/rbTree.c:576:13: warning: function 'rTreeDump' is not needed and will not be emitted [-Wunneeded-internal-declaration]
ucsc/udc.c:1083:60: warning: taking the absolute value of unsigned type 'unsigned long' has no effect [-Wabsolute-value]
ucsc/https.c:76:5: warning: 'ERR_load_SSL_strings' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/rtracklayer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
R 2.0Mb
libs 5.7Mb
* 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
':::' call which should be '::': ‘XVector:::open_input_files’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘GenomicRanges:::INVALID.GR.COLNAMES’
‘S4Vectors:::labeledLine’
‘S4Vectors:::make_XYZxyz_to_XxYyZz_subscript’
‘S4Vectors:::new_SimpleList_from_list’ ‘XVector:::rewind_filexp’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
import,BEDPEFile-ANY-ANY: no visible binding for global variable
‘chrom2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable
‘start2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable ‘end2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable
‘strand2’
Undefined global functions or variables:
chrom2 end2 start2 strand2
* checking Rd files ... WARNING
checkRd: (5) BigBedFile.Rd:96-101: \item in \describe must have non-empty label
checkRd: (5) BigBedSelection.rd:23-30: \item in \describe must have non-empty label
checkRd: (5) BigBedSelection.rd:36-42: \item in \describe must have non-empty label
checkRd: (5) BigWigFile.Rd:137-142: \item in \describe must have non-empty label
checkRd: (5) BigWigFile.Rd:143-172: \item in \describe must have non-empty label
checkRd: (5) BigWigSelection-class.Rd:21-29: \item in \describe must have non-empty label
checkRd: (5) BigWigSelection-class.Rd:35-41: \item in \describe must have non-empty label
checkRd: (5) BrowserViewList-class.Rd:19-22: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:49-55: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:56-59: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:60-62: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:63-65: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:66-69: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:83-88: \item in \describe must have non-empty label
checkRd: (5) GFFFile-class.Rd:248-250: \item in \describe must have non-empty label
checkRd: (5) GenomicData.Rd:24-28: \item in \describe must have non-empty label
checkRd: (5) GenomicData.Rd:29-35: \item in \describe must have non-empty label
checkRd: (5) GenomicData.Rd:41-57: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-methods.Rd:26-30: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:36-43: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:52-55: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:56-57: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:58-60: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:61-63: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:48-72: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:81-86: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:87-90: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:91-94: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:95-98: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:99-102: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:103-106: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:112-114: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:115-117: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:118-120: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:121-123: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:124-150: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:155-159: \item in \describe must have non-empty label
checkRd: (-1) TabixFile-methods.Rd:16: Lost braces
16 | \code{Rsamtools:TabixFile}{TabixFile} objects. These are generally
| ^
checkRd: (5) TrackDb-class.Rd:30-32: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:33-35: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:36-38: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:39-42: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:43-49: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:56-63: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:72-75: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:76-77: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:78-80: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:81-83: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:84-88: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:95-97: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:98-100: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:101-103: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:104-106: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:107-109: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:110-112: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:113-115: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:116-118: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:119-121: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:122-124: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:125-127: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:128-130: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:131-133: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:134-136: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:137-139: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:140-144: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:45-59: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:67-70: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:71-74: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:75-77: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:78-80: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:81-83: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:84-87: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:88-91: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:92-94: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:95-97: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:98-100: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:106-108: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:109-128: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:129-132: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:133-137: \item in \describe must have non-empty label
checkRd: (5) TwoBitFile-class.Rd:106-111: \item in \describe must have non-empty label
checkRd: (5) UCSCSchema-class.Rd:25: \item in \describe must have non-empty label
checkRd: (5) UCSCSchema-class.Rd:26: \item in \describe must have non-empty label
checkRd: (5) UCSCSchema-class.Rd:27: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:92-102: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:110-114: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:115-122: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:123-126: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:135-137: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:138-140: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:141-145: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:146-152: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:153-156: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:157-158: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (-1) layTrack-methods.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) layTrack-methods.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (5) ucscSession-class.Rd:100-105: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘FileForFormat’ ‘Genome’ ‘Track’ ‘TrackContainer’ ‘browserSession<-’
‘cleanupBigBedCache’ ‘descriptionUrl’ ‘descriptionUrl<-’ ‘email’
‘email<-’ ‘genomeField’ ‘genomeField<-’ ‘genomeInfo’ ‘genomeInfo<-’
‘genomesFile’ ‘genomesFile<-’ ‘getTracks’ ‘hub’ ‘hub<-’ ‘hubUrl<-’
‘longLabel’ ‘longLabel<-’ ‘readGFFAsGRanges’ ‘readGFFPragmas’
‘shortLabel’ ‘shortLabel<-’ ‘sniffGFFVersion’ ‘trackField’
‘trackField<-’ ‘trackName’ ‘trackName<-’
Undocumented S4 classes:
‘Track’ ‘RTLFile’ ‘TrackContainer’ ‘RTLFileList’
Undocumented S4 methods:
generic 'as.character' and siglist 'RTLFile'
generic 'browserSession' and siglist 'UCSCTableQuery'
generic 'browserSession<-' and siglist 'UCSCTableQuery'
generic 'export' and siglist 'CompressedGRangesList,BEDFile,ANY'
generic 'export' and siglist 'CompressedGRangesList,GFFFile,ANY'
generic 'export' and siglist 'GRangesList,UCSCFile,ANY'
generic 'export' and siglist 'SimpleGRangesList,BEDFile,ANY'
generic 'export' and siglist 'SimpleGRangesList,GFFFile,ANY'
generic 'export' and siglist 'SimpleGRangesList,WIGFile,ANY'
generic 'fileFormat' and siglist 'Bed15TrackLine'
generic 'fileFormat' and siglist 'GraphTrackLine'
generic 'fileFormat' and siglist 'RTLFile'
generic 'fileFormat' and siglist 'TrackLine'
generic 'genomesFile' and siglist 'TrackHub'
generic 'genomesFile<-' and siglist 'TrackHub'
generic 'initialize' and siglist 'RTLFile'
generic 'liftOver' and siglist 'GRangesList,Chain'
generic 'names' and siglist 'GenomeContainer'
generic 'names' and siglist 'Quickload'
generic 'names' and siglist 'TrackContainer'
generic 'names' and siglist 'TrackHub'
generic 'path' and siglist 'RTLFile'
generic 'show' and siglist 'RTLFile'
generic 'show' and siglist 'UCSCSchema'
generic 'track<-' and siglist 'TrackHubGenome,BiocFile'
generic 'track<-' and siglist 'UCSCSession,SimpleGRangesList'
generic 'trackName' and siglist 'UCSCTableQuery'
generic 'trackName<-' and siglist 'UCSCTableQuery'
generic 'trackNames' and siglist 'QuickloadGenome'
generic 'trackNames' and siglist 'TrackHubGenome'
generic 'trackNames' and siglist 'UCSCTableQuery'
generic 'uri' and siglist 'Quickload'
generic 'uri' and siglist 'TrackHub'
generic 'writeTrackHub' and siglist 'TrackHub'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from Rd file 'ucscView-class.Rd':
Slots for class 'UCSCView'
Code: form hgsid session
Inherited: session
Docs: hgsid session
* checking Rd \usage sections ... OK
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'readGFF.Rd':
‘filter’ ‘raw_data’ ‘GFF1’
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rtracklayer/libs/rtracklayer.so’:
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘__exit’, possibly from ‘_exit’ (C), ‘_Exit’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_rand’, possibly from ‘rand’ (C)
Found ‘_sprintf’, possibly from ‘sprintf’ (C)
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 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 33.367 3.290 38.121
BEDFile-class 7.275 1.402 9.077
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘rtracklayer_unit_tests.R’
ERROR
Running the tests in ‘tests/rtracklayer_unit_tests.R’ failed.
Last 13 lines of output:
1 Test Suite :
rtracklayer RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_ucsc: Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
Test files with failing tests
test_ucsc.R
test_ucsc
Error in BiocGenerics:::testPackage("rtracklayer") :
unit tests failed for package rtracklayer
Calls: <Anonymous> -> <Anonymous>
Execution halted
* 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: 1 ERROR, 5 WARNINGs, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘rtracklayer’ ...
** using staged installation
checking for pkg-config... /opt/R/x86_64/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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readGFF.c -o readGFF.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bbiHelper.c -o bbiHelper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bigWig.c -o bigWig.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bigBedHelper.c -o bigBedHelper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bigBed.c -o bigBed.o
bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable]
bits64 extraIndexListEndOffset = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chain_io.c -o chain_io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c twoBit.c -o twoBit.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c handlers.c -o handlers.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/memgfx.c -o ucsc/memgfx.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o
ucsc/binRange.c:28:12: warning: unused function 'binFromRangeStandard' [-Wunused-function]
static int binFromRangeStandard(int start, int end)
^
ucsc/binRange.c:49:12: warning: unused function 'binFromRangeExtended' [-Wunused-function]
static int binFromRangeExtended(int start, int end)
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/htmlColor.c -o ucsc/htmlColor.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/tokenizer.c -o ucsc/tokenizer.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/asParse.c -o ucsc/asParse.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/basicBed.c -o ucsc/basicBed.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c:150:28: warning: unused function 'bigBedCoverageIntervals' [-Wunused-function]
static struct bbiInterval *bigBedCoverageIntervals(struct bbiFile *bbi,
^
ucsc/bigBed.c:241:31: warning: unused function 'bigBedChunksMatchingName' [-Wunused-function]
static struct fileOffsetSize *bigBedChunksMatchingName(struct bbiFile *bbi,
^
ucsc/bigBed.c:252:31: warning: unused function 'bigBedChunksMatchingNames' [-Wunused-function]
static struct fileOffsetSize *bigBedChunksMatchingNames(struct bbiFile *bbi,
^
ucsc/bigBed.c:301:16: warning: unused function 'bbWordMatchesName' [-Wunused-function]
static boolean bbWordMatchesName(char *line, int fieldIx, void *target)
^
ucsc/bigBed.c:311:16: warning: unused function 'bbWordIsInHash' [-Wunused-function]
static boolean bbWordIsInHash(char *line, int fieldIx, void *target)
^
ucsc/bigBed.c:326:31: warning: unused function 'bigBedIntervalsMatchingName' [-Wunused-function]
static struct bigBedInterval *bigBedIntervalsMatchingName(struct bbiFile *bbi,
^
6 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c:164:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
char *blockPt, *blockEnd;
^
ucsc/bwgQuery.c:47:12: warning: unused function 'bigWigBlockDumpIntersectingRange' [-Wunused-function]
static int bigWigBlockDumpIntersectingRange(boolean isSwapped, char *blockPt, char *blockEnd,
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:530:13: warning: function 'rEnumerateBlocks' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void rEnumerateBlocks(struct cirTreeFile *crt, int level, bits64 indexFileOffset,
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1900:14: warning: unused variable 'naStr' [-Wunused-variable]
static char *naStr = "n/a";
^
ucsc/common.c:1901:14: warning: unused variable 'emptyStr' [-Wunused-variable]
static char *emptyStr = "";
^
ucsc/common.c:1971:13: warning: unused function 'dateAdd' [-Wunused-function]
static void dateAdd(struct tm *tp,int addYears,int addMonths,int addDays)
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:465:12: warning: unused function 'findTailPolyAMaybeMask' [-Wunused-function]
static int findTailPolyAMaybeMask(DNA *dna, int size, boolean doMask,
^
ucsc/dnautil.c:521:12: warning: unused function 'findHeadPolyTMaybeMask' [-Wunused-function]
static int findHeadPolyTMaybeMask(DNA *dna, int size, boolean doMask,
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c:210:13: warning: unused function 'debugAbort' [-Wunused-function]
static void debugAbort()
^
ucsc/errAbort.c:218:13: warning: unused function 'warnAbortHandler' [-Wunused-function]
static void warnAbortHandler(char *format, va_list args)
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/hash.c -o ucsc/hash.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c:14:12: warning: unused variable '_dotForUserMod' [-Wunused-variable]
static int _dotForUserMod = 100; /* How often does dotForUser() output a dot. */
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
ucsc/rangeTree.c:36:14: warning: unused function 'sumInt' [-Wunused-function]
static void *sumInt(void *a, void *b)
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o
ucsc/rbTree.c:576:13: warning: function 'rTreeDump' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void rTreeDump(struct rbTreeNode *n)
^
ucsc/rbTree.c:674:13: warning: unused function 'addRef' [-Wunused-function]
static void addRef(void *item)
^
ucsc/rbTree.c:680:13: warning: unused function 'addRefWithContext' [-Wunused-function]
static void addRefWithContext(void *item, void *context)
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c:220:13: warning: unused function 'carefulMemInit' [-Wunused-function]
static void carefulMemInit(size_t maxToAlloc)
^
ucsc/memalloc.c:314:26: warning: unused variable 'carefulMemHandler' [-Wunused-variable]
static struct memHandler carefulMemHandler =
^
ucsc/memalloc.c:348:13: warning: unused function 'memTrackerFree' [-Wunused-function]
static void memTrackerFree(void *vpt)
^
ucsc/memalloc.c:357:14: warning: unused function 'memTrackerRealloc' [-Wunused-function]
static void *memTrackerRealloc(void *vpt, size_t size)
^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o
ucsc/dlist.c:124:12: warning: unused function 'dlNodeCmp' [-Wunused-function]
static int dlNodeCmp(const void *elem1, const void *elem2)
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/filePath.c -o ucsc/filePath.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/htmlPage.c -o ucsc/htmlPage.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c:1070:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (c = *str++)
~~^~~~~~~~
ucsc/udc.c:1070:14: note: place parentheses around the assignment to silence this warning
while (c = *str++)
^
( )
ucsc/udc.c:1070:14: note: use '==' to turn this assignment into an equality comparison
while (c = *str++)
^
==
ucsc/udc.c:1083:60: warning: taking the absolute value of unsigned type 'unsigned long' has no effect [-Wabsolute-value]
int total_size = url_size + floor(1.0 + log10((double) llabs(hash_id))) + 1;
^
ucsc/udc.c:1083:60: note: remove the call to 'llabs' since unsigned values cannot be negative
int total_size = url_size + floor(1.0 + log10((double) llabs(hash_id))) + 1;
^~~~~
ucsc/udc.c:1273:13: warning: unused function 'qDecode' [-Wunused-function]
static void qDecode(const char *input, char *buf, size_t size)
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/net.c -o ucsc/net.o
ucsc/net.c:36:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
ucsc/net.c:57:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
ucsc/net.c:168:22: warning: unused variable 'status' [-Wunused-variable]
CURLcode status = wrapped_curl_request(curl, GET);
^
ucsc/net.c:187:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/internet.c -o ucsc/internet.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/https.c -o ucsc/https.o
ucsc/https.c:76:5: warning: 'ERR_load_SSL_strings' is deprecated [-Wdeprecated-declarations]
ERR_load_SSL_strings();
^
/opt/R/x86_64/include/openssl/sslerr_legacy.h:29:1: note: 'ERR_load_SSL_strings' has been explicitly marked deprecated here
OSSL_DEPRECATEDIN_3_0 int ERR_load_SSL_strings(void);
^
/opt/R/x86_64/include/openssl/macros.h:194:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0'
# define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0)
^
/opt/R/x86_64/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED'
# define OSSL_DEPRECATED(since) __attribute__((deprecated))
^
ucsc/https.c:22:22: warning: unused function 'openssl_id_callback' [-Wunused-function]
static unsigned long openssl_id_callback(void)
^
ucsc/https.c:27:13: warning: unused function 'openssl_locking_callback' [-Wunused-function]
static void openssl_locking_callback(int mode, int n, const char * file, int line)
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/os.c -o ucsc/os.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread /opt/R/x86_64/lib/libssl.a /opt/R/x86_64/lib/libcrypto.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/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.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'BiocIO'
The following object is masked from 'package:rtracklayer':
FileForFormat
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Timing stopped at: 28.92 1.779 55.13
Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
In addition: There were 16 warnings (use warnings() to see them)
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig
RUNIT TEST PROTOCOL -- Fri Dec 20 09:06:08 2024
***********************************************
Number of test functions: 11
Number of errors: 1
Number of failures: 0
1 Test Suite :
rtracklayer RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_ucsc: Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
Test files with failing tests
test_ucsc.R
test_ucsc
Error in BiocGenerics:::testPackage("rtracklayer") :
unit tests failed for package rtracklayer
Calls: <Anonymous> -> <Anonymous>
Execution halted
rtracklayer.Rcheck/rtracklayer-Ex.timings
| name | user | system | elapsed | |
| BEDFile-class | 7.275 | 1.402 | 9.077 | |
| BamFile-methods | 0.237 | 0.032 | 0.283 | |
| BigBedFile | 0.706 | 0.086 | 0.819 | |
| BigBedSelection | 0.052 | 0.003 | 0.061 | |
| BigWigFile | 33.367 | 3.290 | 38.121 | |
| BigWigSelection-class | 0.039 | 0.003 | 0.045 | |
| GFFFile-class | 2.484 | 0.304 | 2.871 | |
| GenomicData | 0.350 | 0.019 | 0.373 | |
| GenomicSelection | 0.316 | 0.017 | 0.396 | |
| Quickload-class | 0.263 | 0.019 | 0.338 | |
| QuickloadGenome-class | 0.359 | 0.014 | 0.396 | |
| TrackHub-class | 0.080 | 0.004 | 0.086 | |
| TrackHubGenome-class | 0.030 | 0.003 | 0.033 | |
| TwoBitFile-class | 0.177 | 0.006 | 0.190 | |
| UCSCSchema-class | 0.001 | 0.000 | 0.001 | |
| UCSCTableQuery-class | 0.001 | 0.002 | 0.002 | |
| WIGFile-class | 1.938 | 0.051 | 2.063 | |
| asBED | 0.000 | 0.000 | 0.001 | |
| asGFF | 0.000 | 0.000 | 0.001 | |
| browseGenome | 0.000 | 0.001 | 0.000 | |
| browserView-methods | 0.001 | 0.001 | 0.001 | |
| browserViews-methods | 0.000 | 0.000 | 0.001 | |
| cpneTrack | 1.088 | 0.166 | 1.356 | |
| layTrack-methods | 0.000 | 0.001 | 0.001 | |
| liftOver | 0.000 | 0.000 | 0.001 | |
| readGFF | 0.745 | 0.025 | 0.776 | |
| targets | 0.084 | 0.009 | 0.095 | |
| ucscGenomes | 0.520 | 0.027 | 1.141 | |
| ucscTrackModes-methods | 0.025 | 0.001 | 0.026 | |