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This page was generated on 2025-03-11 15:34 -0400 (Tue, 11 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 869
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Package 180/217HostnameOS / ArchINSTALLBUILDCHECK
rtracklayer 1.67.1  (landing page)
Michael Lawrence
Snapshot Date: 2025-03-11 12:00 -0400 (Tue, 11 Mar 2025)
git_url: https://git.bioconductor.org/packages/rtracklayer
git_branch: devel
git_last_commit: a2eb6fd
git_last_commit_date: 2025-03-08 10:13:08 -0400 (Sat, 08 Mar 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  

CHECK results for rtracklayer on teran2

To the developers/maintainers of the rtracklayer package:
- 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.

raw results


Summary

Package: rtracklayer
Version: 1.67.1
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings rtracklayer_1.67.1.tar.gz
StartedAt: 2025-03-11 15:02:06 -0400 (Tue, 11 Mar 2025)
EndedAt: 2025-03-11 15:07:19 -0400 (Tue, 11 Mar 2025)
EllapsedTime: 312.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rtracklayer.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings rtracklayer_1.67.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/rtracklayer.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.67.1’
* 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:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
  ucsc/basicBed.c:449:1: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
  ucsc/udc.c:936:26: warning: ‘%02X’ directive output may be truncated writing between 2 and 8 bytes into a region of size 2 [-Wformat-truncation=]
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/rtracklayer.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
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 '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 ... NOTE
Note: information on .o files is not available
File ‘rtracklayer/libs/rtracklayer.so’:
  Found non-API calls to R: ‘R_ReadConnection’, ‘R_ignore_SIGPIPE’,
    ‘getConnection’

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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
BigWigFile 16.974  5.776  23.072
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 6 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/rtracklayer.Rcheck/00check.log’
for details.

Installation output

rtracklayer.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL rtracklayer
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘rtracklayer’ ...
** this is package ‘rtracklayer’ version ‘1.67.1’
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c readGFF.c -o readGFF.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bbiHelper.c -o bbiHelper.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:268:11: warning: ‘ans_nhits’ may be used uninitialized [-Wmaybe-uninitialized]
  268 |           INTEGER(ans_nhits)[i] = nqhits;
      |           ^~~~~~~~~~~~~~~~~~
bigWig.c:231:58: note: ‘ans_nhits’ was declared here
  231 |   SEXP ans, ans_start, ans_width, ans_score, ans_ranges, ans_nhits;
      |                                                          ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bigBedHelper.c -o bigBedHelper.o
In file included from /usr/include/string.h:548,
                 from ucsc/common.h:33,
                 from bigBedHelper.h:5,
                 from bigBedHelper.c:1:
In function ‘strncpy’,
    inlined from ‘bbNamedFileChunkKey’ at bigBedHelper.c:148:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
   95 |   return __builtin___strncpy_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   96 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bigBed.c -o bigBed.o
bigBed.c: In function ‘BBDFile_query’:
bigBed.c:195:7: warning: ‘name’ may be used uninitialized [-Wmaybe-uninitialized]
  195 |       SET_STRING_ELT(name, i, mkChar(bed->name));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:74:54: note: ‘name’ was declared here
   74 |   SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
      |                                                      ^~~~
bigBed.c:198:7: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized]
  198 |       INTEGER(score)[i] = bed->score;
      |       ^~~~~~~~~~~~~~
bigBed.c:74:60: note: ‘score’ was declared here
   74 |   SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
      |                                                            ^~~~~
bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized [-Wmaybe-uninitialized]
  205 |       INTEGER(thickStart)[i] = bed->thickStart;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:26: note: ‘thickStart’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                          ^~~~~~~~~~
bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized [-Wmaybe-uninitialized]
  204 |       INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:38: note: ‘thickWidth’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                                      ^~~~~~~~~~
bigBed.c:209:7: warning: ‘itemRgb’ may be used uninitialized [-Wmaybe-uninitialized]
  209 |       SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:50: note: ‘itemRgb’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                                                  ^~~~~~~
bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized [-Wmaybe-uninitialized]
  218 |       SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:59: note: ‘blocks’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                                                           ^~~~~~
bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized [-Wmaybe-uninitialized]
  236 |             INTEGER(lengthIndex)[efIndex] = index + 1;
      |             ^~~~~~~~~~~~~~~~~~~~
bigBed.c:76:31: note: ‘lengthIndex’ was declared here
   76 |     extraFields = R_NilValue, lengthIndex;
      |                               ^~~~~~~~~~~
bigBed.c:226:22: warning: ‘typeId’ may be used uninitialized [-Wmaybe-uninitialized]
  226 |         switch(typeId[efIndex]) {
      |                      ^
bigBed.c:141:13: note: ‘typeId’ was declared here
  141 |   SEXPTYPE *typeId;
      |             ^~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c chain_io.c -o chain_io.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c twoBit.c -o twoBit.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c handlers.c -o handlers.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/memgfx.c -o ucsc/memgfx.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/asParse.c -o ucsc/asParse.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function ‘bedParseRgb’:
ucsc/basicBed.c:449:1: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
  449 | strncpy(dupe, itemRgb, sizeof(dupe));
      | ^
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bigBed.c -o ucsc/bigBed.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/common.c -o ucsc/common.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/errAbort.c -o ucsc/errAbort.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/filePath.c -o ucsc/filePath.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘qEncode’:
ucsc/udc.c:936:26: warning: ‘%02X’ directive output may be truncated writing between 2 and 8 bytes into a region of size 2 [-Wformat-truncation=]
  936 |         snprintf(d, 3, "Q%02X", (unsigned)c);
      |                          ^~~~
ucsc/udc.c:936:24: note: directive argument in the range [1, 4294967295]
  936 |         snprintf(d, 3, "Q%02X", (unsigned)c);
      |                        ^~~~~~~
In file included from /usr/include/stdio.h:980,
                 from ucsc/common.h:30,
                 from ucsc/udc.c:34:
In function ‘snprintf’,
    inlined from ‘qEncode’ at ucsc/udc.c:936:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: note: ‘__builtin___snprintf_chk’ output between 4 and 10 bytes into a destination of size 3
   54 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   55 |                                    __glibc_objsize (__s), __fmt,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   56 |                                    __va_arg_pack ());
      |                                    ~~~~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/net.c -o ucsc/net.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/internet.c -o ucsc/internet.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/https.c -o ucsc/https.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -lssl -lcrypto -lcurl
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rtracklayer)

Tests output

rtracklayer.Rcheck/tests/rtracklayer_unit_tests.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
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 -- Tue Mar 11 15:06:48 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 
 31.870   1.718  63.782

Example timings

rtracklayer.Rcheck/rtracklayer-Ex.timings

nameusersystemelapsed
BEDFile-class2.0880.1432.243
BamFile-methods0.0660.0260.092
BigBedFile0.1660.0770.244
BigBedSelection0.0150.0060.020
BigWigFile16.974 5.77623.072
BigWigSelection-class0.0110.0010.012
GFFFile-class0.6810.1260.811
GenomicData0.3310.0072.238
GenomicSelection0.0580.0030.061
Quickload-class0.0100.0010.012
QuickloadGenome-class0.0570.0000.059
TrackHub-class0.0240.0010.027
TrackHubGenome-class0.0090.0000.009
TwoBitFile-class0.0520.0000.053
UCSCSchema-class000
UCSCTableQuery-class000
WIGFile-class0.5230.0110.534
asBED000
asGFF000
browseGenome000
browserView-methods000
browserViews-methods000
cpneTrack0.4630.0280.491
layTrack-methods000
liftOver000
readGFF0.1920.0010.193
targets0.0470.0020.049
ucscGenomes0.1580.0030.607
ucscTrackModes-methods0.0120.0000.012