Michael Lawrence
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/rtracklayer |
| Branch: master |
| Last Commit: 7f10f22 |
| Last Changed Date: 2019-10-29 13:34:49 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:31:15 -0500 (Thu, 16 Jan 2020).
| Package 1490/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rtracklayer 1.47.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: rtracklayer |
| Version: 1.47.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rtracklayer_1.47.0.tar.gz |
| StartedAt: 2020-01-16 08:28:44 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 08:35:34 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 409.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rtracklayer.Rcheck |
| Warnings: 3 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rtracklayer_1.47.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rtracklayer.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.47.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rtracklayer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.7Mb
libs 2.4Mb
* 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.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘RTLFileList’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readIGVDataFile: no visible global function definition for
‘xmlTreeParse’
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 xmlTreeParse
* 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’
Undocumented S4 methods:
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 'TrackLine'
generic 'liftOver' and siglist 'GRangesList,Chain'
generic 'track<-' and siglist 'UCSCSession,SimpleGRangesList'
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 ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rtracklayer/libs/rtracklayer.so’:
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘__exit’, possibly from ‘_exit’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘_rand’, possibly from ‘rand’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BigWigFile 31.194 7.561 38.761
BEDFile-class 6.287 0.841 7.137
* 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, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
rtracklayer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rtracklayer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘rtracklayer’ ... ** using staged installation checking for pkg-config... /usr/local/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 clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c readGFF.c -o readGFF.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bigWig.c -o bigWig.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chain_io.c -o chain_io.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c twoBit.c -o twoBit.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c handlers.c -o handlers.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/errAbort.c -o ucsc/errAbort.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/hash.c -o ucsc/hash.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/udc.c -o ucsc/udc.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/net.c -o ucsc/net.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/internet.c -o ucsc/internet.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/https.c -o ucsc/https.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/os.c -o ucsc/os.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2r/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /usr/local/Cellar/openssl/1.0.2r/lib/libssl.a /usr/local/Cellar/openssl/1.0.2r/lib/libcrypto.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-rtracklayer/00new/rtracklayer/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’ 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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rtracklayer)
rtracklayer.Rcheck/tests/rtracklayer_unit_tests.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> 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, 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, 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 -- Thu Jan 16 08:35:20 2020
***********************************************
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
47.847 2.438 50.607
rtracklayer.Rcheck/rtracklayer-Ex.timings
| name | user | system | elapsed | |
| BEDFile-class | 6.287 | 0.841 | 7.137 | |
| BamFile-methods | 0.272 | 0.023 | 0.296 | |
| BigWigFile | 31.194 | 7.561 | 38.761 | |
| BigWigSelection-class | 0.036 | 0.001 | 0.037 | |
| GFFFile-class | 2.376 | 0.172 | 2.550 | |
| GenomicData | 0.270 | 0.026 | 0.297 | |
| GenomicSelection | 0.249 | 0.025 | 0.274 | |
| Quickload-class | 0.378 | 0.272 | 1.011 | |
| QuickloadGenome-class | 0.388 | 0.007 | 0.398 | |
| TwoBitFile-class | 0.115 | 0.004 | 0.120 | |
| UCSCSchema-class | 0.001 | 0.000 | 0.001 | |
| UCSCTableQuery-class | 0.000 | 0.000 | 0.001 | |
| WIGFile-class | 1.609 | 0.025 | 1.637 | |
| asBED | 0.001 | 0.000 | 0.000 | |
| asGFF | 0.000 | 0.000 | 0.001 | |
| browseGenome | 0.000 | 0.001 | 0.001 | |
| browserView-methods | 0.001 | 0.001 | 0.001 | |
| browserViews-methods | 0.000 | 0.000 | 0.001 | |
| cpneTrack | 0.444 | 0.047 | 0.492 | |
| export | 0.116 | 0.012 | 0.130 | |
| layTrack-methods | 0.001 | 0.000 | 0.001 | |
| liftOver | 0 | 0 | 0 | |
| readGFF | 0.718 | 0.017 | 0.764 | |
| targets | 0.082 | 0.009 | 0.091 | |
| ucscGenomes | 0.283 | 0.013 | 0.839 | |
| ucscTrackModes-methods | 0.025 | 0.001 | 0.026 | |