rtracklayer 1.32.2
Michael Lawrence
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/rtracklayer | | Last Changed Rev: 119616 / Revision: 122332 | | Last Changed Date: 2016-07-25 05:01:37 -0700 (Mon, 25 Jul 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rtracklayer_1.32.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/rtracklayer.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.32.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rtracklayer’ can be installed ... OK
* 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
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:::open_input_files’
‘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,BEDFile-ANY-ANY: warning in rgb(cols[1, ], cols[2, ], cols[3, ],
max = 255): partial argument match of 'max' to 'maxColorValue'
asGTF,GRangesList : processFeatures: no visible binding for global
variable ‘tx_id’
asGTF,GRangesList: no visible global function definition for
‘pmapFromTranscripts’
asGTF,GRangesList: no visible global function definition for
‘rectifyDataFrame’
export,GAlignmentPairs-BamFile-ANY : getMateAttribute: no visible
global function definition for ‘last’
export,GenomicRanges-GFFFile-ANY: no visible global function definition
for ‘package.version’
getSeq,TwoBitFile: no visible binding for global variable ‘con’
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’
intersectTrack<-,UCSCTableQuery: possible error in normArgTrack(value,
x, TRUE): unused argument (TRUE)
Undefined global functions or variables:
chrom2 con end2 last package.version pmapFromTranscripts
rectifyDataFrame start2 strand2 tx_id
* checking Rd files ... NOTE
prepare_Rd: readGFF.Rd:52-53: Dropping empty section \details
prepare_Rd: readGFF.Rd:55-56: Dropping empty section \value
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘cleanupBigWigCache’ ‘readGFFAsGRanges’ ‘readGFFPragmas’
‘sniffGFFVersion’
Undocumented S4 classes:
‘RTLFileList’
Undocumented S4 methods:
generic 'as.character' and siglist 'RTLFile'
generic 'export' and siglist 'ANY,BEDPEFile,ANY'
generic 'export' and siglist 'GRangesList,GTFFile,ANY'
generic 'export' and siglist 'Pairs,BEDPEFile,ANY'
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 ... 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 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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘rtracklayer/libs/rtracklayer.so’:
Found ‘_exit’, possibly from ‘_exit’ (C)
Object: ‘ucsc/os.o’
Found ‘abort’, possibly from ‘abort’ (C)
Object: ‘ucsc/errAbort.o’
Found ‘exit’, possibly from ‘exit’ (C)
Objects: ‘ucsc/errAbort.o’, ‘ucsc/pipeline.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Object: ‘ucsc/pipeline.o’
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘ucsc/obscure.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Objects: ‘ucsc/errAbort.o’, ‘ucsc/obscure.o’, ‘ucsc/pipeline.o’,
‘ucsc/net.o’, ‘ucsc/https.o’, ‘ucsc/verbose.o’, ‘ucsc/os.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Objects: ‘ucsc/common.o’, ‘ucsc/errAbort.o’, ‘ucsc/net.o’,
‘ucsc/https.o’, ‘ucsc/verbose.o’, ‘ucsc/os.o’
File ‘rtracklayer/libs/rtracklayer.so’:
Found non-API calls to R: ‘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 the system RNG.
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BigWigFile 6.265 2.546 8.848
* 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-3.3-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
* installing *source* package ‘rtracklayer’ ...
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 -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c readGFF.c -o readGFF.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c chain_io.c -o chain_io.o
chain_io.c: In function ‘read_chain_file’:
chain_io.c:119:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(linebuf, LINEBUF_SIZE, stream); /* skip empty line */
^
chain_io.c:116:24: warning: ‘header_line’ may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(block->length, IntAE_get_nelt(block->length),
^
chain_io.c:101:22: warning: ‘block’ may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(block->offset, IntAE_get_nelt(block->offset),
^
chain_io.c:110:12: warning: ‘qrc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (qrc)
^
chain_io.c:106:12: warning: ‘trc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trc) /* width already subtracted above */
^
chain_io.c:98:14: warning: ‘qstart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
qstart -= (qrc ? width : 0);
^
chain_io.c:97:14: warning: ‘tstart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
tstart -= (trc ? width : 0);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c handlers.c -o handlers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_STRSXP_collapse’:
utils.c:4:8: warning: unused variable ‘ans’ [-Wunused-variable]
SEXP ans;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function ‘bptDataStart’:
ucsc/bPlusTree.c:286:12: warning: variable ‘childCount’ set but not used [-Wunused-but-set-variable]
bits16 childCount;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function ‘bbiTotalSummary’:
ucsc/bbiRead.c:748:34: warning: variable ‘chromEnd’ set but not used [-Wunused-but-set-variable]
bits32 chromId, chromStart, chromEnd;
^
ucsc/bbiRead.c:748:22: warning: variable ‘chromStart’ set but not used [-Wunused-but-set-variable]
bits32 chromId, chromStart, chromEnd;
^
ucsc/bbiRead.c:748:13: warning: variable ‘chromId’ set but not used [-Wunused-but-set-variable]
bits32 chromId, chromStart, chromEnd;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/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]
char *blockPt, *blockEnd;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function ‘reverseComplementSlashSeparated’:
ucsc/dnautil.c:496:5: warning: implicit declaration of function ‘isAllNt’ [-Wimplicit-function-declaration]
if (isAllNt(allele, alLen))
^
ucsc/dnautil.c: In function ‘findHeadPolyTMaybeMask’:
ucsc/dnautil.c:977:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable]
int pastPoly = 0;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function ‘getThreadVars’:
ucsc/errAbort.c:331:10: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
write(STDERR_FILENO, errMsg, strlen(errMsg));
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcBitmapOpen’:
ucsc/udc.c:570:8: warning: variable ‘reserved64’ set but not used [-Wunused-but-set-variable]
bits64 reserved64;
^
ucsc/udc.c:569:8: warning: variable ‘reserved32’ set but not used [-Wunused-but-set-variable]
bits32 reserved32;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o
ucsc/net.c: In function ‘netSkipHttpHeaderLinesWithRedirect’:
ucsc/net.c:1448:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable]
char *version, *code;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-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 bigWig.o chain_io.o twoBit.o handlers.o utils.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/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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)