Michael Lawrence
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rtracklayer |
| Branch: RELEASE_3_9 |
| Last Commit: aec96e8 |
| Last Changed Date: 2019-09-06 10:43:31 -0400 (Fri, 06 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:46:55 -0400 (Wed, 16 Oct 2019).
| Package 1435/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rtracklayer 1.44.4 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.44.4 |
| 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_1.44.4.tar.gz |
| StartedAt: 2019-10-16 06:28:27 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:34:56 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 389.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rtracklayer.Rcheck |
| Warnings: 3 |
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### Running 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_1.44.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rtracklayer.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.44.4’
* 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.
* 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 ‘/Library/Frameworks/R.framework/Versions/3.6/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 or elapsed time > 5s
user system elapsed
BigWigFile 34.009 8.755 43.271
BEDFile-class 5.910 0.757 6.676
* 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-3.9-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/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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 clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] installing to /Library/Frameworks/R.framework/Versions/3.6/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
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, 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 -- Wed Oct 16 06:34:42 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
38.587 2.332 41.176
rtracklayer.Rcheck/rtracklayer-Ex.timings
| name | user | system | elapsed | |
| BEDFile-class | 5.910 | 0.757 | 6.676 | |
| BamFile-methods | 0.266 | 0.014 | 0.281 | |
| BigWigFile | 34.009 | 8.755 | 43.271 | |
| BigWigSelection-class | 0.034 | 0.001 | 0.036 | |
| GFFFile-class | 1.733 | 0.127 | 1.864 | |
| GenomicData | 0.270 | 0.033 | 0.304 | |
| GenomicSelection | 0.265 | 0.363 | 0.630 | |
| Quickload-class | 0.340 | 0.027 | 0.740 | |
| QuickloadGenome-class | 0.379 | 0.009 | 0.392 | |
| TwoBitFile-class | 0.111 | 0.003 | 0.115 | |
| UCSCSchema-class | 0.001 | 0.000 | 0.001 | |
| UCSCTableQuery-class | 0.000 | 0.000 | 0.002 | |
| WIGFile-class | 1.270 | 0.028 | 1.324 | |
| asBED | 0.000 | 0.001 | 0.000 | |
| asGFF | 0.000 | 0.000 | 0.001 | |
| browseGenome | 0.001 | 0.001 | 0.000 | |
| browserView-methods | 0.001 | 0.000 | 0.000 | |
| browserViews-methods | 0 | 0 | 0 | |
| cpneTrack | 0.423 | 0.117 | 0.541 | |
| export | 0.120 | 0.204 | 0.325 | |
| layTrack-methods | 0.000 | 0.000 | 0.001 | |
| liftOver | 0.001 | 0.000 | 0.001 | |
| readGFF | 0.528 | 0.014 | 0.543 | |
| targets | 0.073 | 0.011 | 0.084 | |
| ucscGenomes | 0.259 | 0.014 | 0.667 | |
| ucscTrackModes-methods | 0.023 | 0.000 | 0.024 | |