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This page was generated on 2022-06-24 12:05:20 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for rtracklayer on nebbiolo1


To the developers/maintainers of the rtracklayer package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1722/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.56.1  (landing page)
Michael Lawrence
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/rtracklayer
git_branch: RELEASE_3_15
git_last_commit: 4c6d220
git_last_commit_date: 2022-06-22 15:10:46 -0400 (Wed, 22 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: rtracklayer
Version: 1.56.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings rtracklayer_1.56.1.tar.gz
StartedAt: 2022-06-23 21:48:49 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:53:17 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 267.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rtracklayer.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings rtracklayer_1.56.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/rtracklayer.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.56.1’
* 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:106:10: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
  ucsc/bigBed.c:314:2: warning: ‘%s’ directive argument is null [-Wformat-overflow=]
  ucsc/errAbort.c:331:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  ucsc/net.c:148:31: warning: passing argument 3 to restrict-qualified parameter aliases with argument 4 [-Wrestrict]
See ‘/home/biocbuild/bbs-3.15-bioc/meat/rtracklayer.Rcheck/00install.out’ for details.
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... OK
* 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’
  ‘resource’ ‘shortLabel’ ‘shortLabel<-’ ‘sniffGFFVersion’ ‘trackField’
  ‘trackField<-’ ‘trackName’ ‘trackName<-’
Undocumented S4 classes:
  ‘RTLFile’ ‘Track’ ‘TrackContainer’ ‘RTLFileList’
Undocumented S4 methods:
  generic 'as.character' and siglist 'RTLFile'
  generic 'browserSession' and siglist 'UCSCTableQuery'
  generic 'browserSession<-' and siglist 'UCSCTableQuery'
  generic 'export' and siglist 'CompressedGRangesList,BEDFile,ANY'
  generic 'export' and siglist 'CompressedGRangesList,GFFFile,ANY'
  generic 'export' and siglist 'GRangesList,UCSCFile,ANY'
  generic 'export' and siglist 'SimpleGRangesList,BEDFile,ANY'
  generic 'export' and siglist 'SimpleGRangesList,GFFFile,ANY'
  generic 'export' and siglist 'SimpleGRangesList,WIGFile,ANY'
  generic 'fileFormat' and siglist 'Bed15TrackLine'
  generic 'fileFormat' and siglist 'GraphTrackLine'
  generic 'fileFormat' and siglist 'RTLFile'
  generic 'fileFormat' and siglist 'TrackLine'
  generic 'genomesFile' and siglist 'TrackHub'
  generic 'genomesFile<-' and siglist 'TrackHub'
  generic 'initialize' and siglist 'RTLFile'
  generic 'liftOver' and siglist 'GRangesList,Chain'
  generic 'names' and siglist 'GenomeContainer'
  generic 'names' and siglist 'Quickload'
  generic 'names' and siglist 'TrackContainer'
  generic 'names' and siglist 'TrackHub'
  generic 'path' and siglist 'RTLFile'
  generic 'show' and siglist 'RTLFile'
  generic 'show' and siglist 'UCSCSchema'
  generic 'track<-' and siglist 'TrackHubGenome,BiocFile'
  generic 'track<-' and siglist 'UCSCSession,SimpleGRangesList'
  generic 'trackName' and siglist 'UCSCTableQuery'
  generic 'trackName<-' and siglist 'UCSCTableQuery'
  generic 'trackNames' and siglist 'QuickloadGenome'
  generic 'trackNames' and siglist 'TrackHubGenome'
  generic 'trackNames' and siglist 'UCSCTableQuery'
  generic 'uri' and siglist 'Quickload'
  generic 'uri' and siglist 'TrackHub'
  generic 'writeTrackHub' and siglist 'TrackHub'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'UCSCView-class':
Slots for class 'UCSCView'
  Code: form hgsid session
  Inherited: session
  Docs: hgsid session

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.15-bioc/R/library/rtracklayer/libs/rtracklayer.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rtracklayer/libs/rtracklayer.so’:
  Found non-API calls to R: ‘R_ReadConnection’, ‘R_ignore_SIGPIPE’,
    ‘getConnection’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
BigWigFile 20.476  5.391  25.871
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘rtracklayer_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.



Installation output

rtracklayer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘rtracklayer’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c readGFF.c -o readGFF.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bbiHelper.c -o bbiHelper.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bigWig.c -o bigWig.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bigBedHelper.c -o bigBedHelper.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bigBed.c -o bigBed.o
bigBed.c: In function ‘BBDFile_write’:
bigBed.c:338:10: warning: variable ‘extraIndexListEndOffset’ set but not used [-Wunused-but-set-variable]
  338 |   bits64 extraIndexListEndOffset = 0;
      |          ^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function ‘BBDFile_query’:
bigBed.c:226:22: warning: ‘typeId’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  226 |         switch(typeId[efIndex]) {
      |                      ^
bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  236 |             INTEGER(lengthIndex)[efIndex] = index + 1;
      |             ^~~~~~~~~~~~~~~~~~~~
bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  218 |       SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:209:7: warning: ‘itemRgb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  209 |       SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  204 |       INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  205 |       INTEGER(thickStart)[i] = bed->thickStart;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:198:7: warning: ‘score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  198 |       INTEGER(score)[i] = bed->score;
      |       ^~~~~~~~~~~~~~
bigBed.c:257:5: warning: ‘name’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  257 |     SET_VECTOR_ELT(ans, index++, name);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c chain_io.c -o chain_io.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c twoBit.c -o twoBit.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c handlers.c -o handlers.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/memgfx.c -o ucsc/memgfx.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/aliType.c -o ucsc/aliType.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/asParse.c -o ucsc/asParse.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/basicBed.c -o ucsc/basicBed.o
In file included from /usr/include/string.h:495,
                 from ucsc/common.h:33,
                 from ucsc/basicBed.c:14:
In function ‘strncpy’,
    inlined from ‘bedParseRgb’ at ucsc/basicBed.c:997:1:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c: In function ‘extractField’:
ucsc/bigBed.c:314:2: warning: ‘%s’ directive argument is null [-Wformat-overflow=]
  314 |  warn("Not enough fields in extractField of %s", line);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function ‘bigWigIntervalQuery’:
ucsc/bwgQuery.c:187:18: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable]
  187 |  char *blockPt, *blockEnd;
      |                  ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/common.c -o ucsc/common.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function ‘getThreadVars’:
ucsc/errAbort.c:331:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  331 |     write(STDERR_FILENO, errMsg, strlen(errMsg));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/hex.c -o ucsc/hex.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/filePath.c -o ucsc/filePath.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/udc.c -o ucsc/udc.o
In file included from ucsc/udc.c:41:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
  178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
      |  
ucsc/udc.c: In function ‘djb2_hash’:
ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 1088 |     while (c = *str++)
      |            ^
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/net.c -o ucsc/net.o
In file included from ucsc/net.c:19:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
  178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
      |  
ucsc/net.c: In function ‘netConnectWithTimeout’:
ucsc/net.c:148:31: warning: passing argument 3 to restrict-qualified parameter aliases with argument 4 [-Wrestrict]
  148 |      res = select(sd+1, NULL, &mySet, &mySet, &tempTime);
      |                               ^~~~~~  ~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
In file included from ucsc/twoBit.c:15:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
  178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
      |  
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/internet.c -o ucsc/internet.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
In file included from ucsc/https.c:17:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
  178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
      |  
ucsc/https.c:27:13: warning: ‘openssl_locking_callback’ defined but not used [-Wunused-function]
   27 | static void openssl_locking_callback(int mode, int n, const char * file, int line)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~
ucsc/https.c:22:22: warning: ‘openssl_id_callback’ defined but not used [-Wunused-function]
   22 | static unsigned long openssl_id_callback(void)
      |                      ^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -lssl -lcrypto -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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 version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following 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 -- Thu Jun 23 21:53:12 2022 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rtracklayer RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
There were 16 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 34.710   2.097  54.399 

Example timings

rtracklayer.Rcheck/rtracklayer-Ex.timings

nameusersystemelapsed
BEDFile-class3.5180.3043.823
BamFile-methods0.1110.0040.116
BigBedFile0.2640.0160.282
BigBedSelection0.0250.0000.026
BigWigFile20.476 5.39125.871
BigWigSelection-class0.0150.0040.018
GFFFile-class1.0660.2601.326
GenomicData0.1510.0280.178
GenomicSelection0.1510.0040.155
Quickload-class0.1650.0030.373
QuickloadGenome-class0.1650.0040.169
TrackHub-class0.0390.0000.039
TrackHubGenome-class0.0100.0040.014
TwoBitFile-class0.0780.0000.078
UCSCSchema-class0.0010.0000.000
UCSCTableQuery-class0.0010.0000.000
WIGFile-class0.8270.0280.855
asBED000
asGFF000
browseGenome0.0010.0000.000
browserView-methods0.0010.0000.000
browserViews-methods000
cpneTrack1.0340.0471.081
layTrack-methods000
liftOver000
readGFF0.2900.0160.306
targets0.0440.0040.049
ucscGenomes0.2020.0281.101
ucscTrackModes-methods0.0170.0000.017