Package: rtracklayer

Version: 1.42.2

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings rtracklayer_1.42.2.tar.gz

StartedAt: 2019-04-16 02:48:48 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:52:43 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 234.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: rtracklayer.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings rtracklayer_1.42.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/rtracklayer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.42.2’
* 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
':::' 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
smoothGaps: no visible binding for global variable ‘congruent’
export,DNAStringSet-TwoBitFile-ANY: no visible global function
  definition for ‘uniqueLetters’
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 congruent end2 start2 strand2 uniqueLetters
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IntegerRangesList-methods.Rd':
  ‘[IRanges]{names}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘readGFFAsGRanges’ ‘readGFFPragmas’ ‘sniffGFFVersion’
All user-level objects in a package 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/rtracklayer/libs/rtracklayer.so’:
  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 or elapsed time > 5s
             user system elapsed
BigWigFile 23.408  3.684   27.15
* 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-3.8-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL rtracklayer
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* 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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c readGFF.c -o readGFF.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:280:4: warning: ‘ans_nhits’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    INTEGER(ans_nhits)[i] = nqhits;
    ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c twoBit.c -o twoBit.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c handlers.c -o handlers.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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]
  char *blockPt, *blockEnd;
                  ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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]
     write(STDERR_FILENO, errMsg, strlen(errMsg)); 
     ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/udc.c -o ucsc/udc.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/net.c -o ucsc/net.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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’
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)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

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 Apr 16 02:52:33 2019 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rtracklayer RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
There were 14 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 29.868   0.696  31.244 

name	user	system	elapsed
BEDFile-class	3.256	0.148	3.426
BamFile-methods	0.200	0.012	0.213
BigWigFile	23.408	3.684	27.150
BigWigSelection-class	0.02	0.00	0.02
GFFFile-class	1.052	0.068	1.127
GenomicData	0.192	0.000	0.193
GenomicSelection	0.212	0.000	0.213
Quickload-class	0.400	0.020	0.977
QuickloadGenome-class	0.272	0.008	0.287
TwoBitFile-class	0.100	0.000	0.109
UCSCSchema-class	0.000	0.000	0.001
UCSCTableQuery-class	0	0	0
WIGFile-class	1.168	0.008	1.187
asBED	0	0	0
asGFF	0	0	0
browseGenome	0	0	0
browserView-methods	0	0	0
browserViews-methods	0	0	0
cpneTrack	0.508	0.016	0.550
export	0.076	0.000	0.099
layTrack-methods	0.000	0.000	0.001
liftOver	0	0	0
readGFF	0.516	0.000	0.522
targets	0.076	0.000	0.077
ucscGenomes	0.196	0.000	0.899
ucscTrackModes-methods	0.024	0.000	0.022