Michael Lawrence
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/rtracklayer |
| Branch: RELEASE_3_7 |
| Last Commit: ba9a6e7 |
| Last Changed Date: 2018-08-30 18:09:48 -0400 (Thu, 30 Aug 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:22:23 -0400 (Wed, 17 Oct 2018).
| Package 1295/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rtracklayer 1.40.6 Michael Lawrence
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: rtracklayer |
| Version: 1.40.6 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings rtracklayer_1.40.6.tar.gz |
| StartedAt: 2018-10-16 03:29:37 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 03:33:04 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 207.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rtracklayer.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings rtracklayer_1.40.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/rtracklayer.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.40.6’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rtracklayer’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Artistic-2.0 + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘GenomicRanges:::INVALID.GR.COLNAMES’
‘S4Vectors:::labeledLine’
‘S4Vectors:::make_XYZxyz_to_XxYyZz_subscript’
‘S4Vectors:::new_SimpleList_from_list’ ‘XVector:::open_input_files’
‘XVector:::rewind_filexp’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
smoothGaps: no visible binding for global variable ‘congruent’
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
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in 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-3.7-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 27.684 3.72 31.562
* 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: 2 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
rtracklayer.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c readGFF.c -o readGFF.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c handlers.c -o handlers.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-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)
rtracklayer.Rcheck/tests/rtracklayer_unit_tests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 16 03:33:00 2018
***********************************************
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
25.40 0.66 26.27
rtracklayer.Rcheck/rtracklayer-Ex.timings
| name | user | system | elapsed | |
| BEDFile-class | 2.900 | 0.148 | 3.062 | |
| BamFile-methods | 0.092 | 0.012 | 0.104 | |
| BigWigFile | 27.684 | 3.720 | 31.562 | |
| BigWigSelection-class | 0.020 | 0.000 | 0.021 | |
| GFFFile-class | 1.276 | 0.028 | 1.309 | |
| GenomicData | 0.176 | 0.000 | 0.175 | |
| GenomicSelection | 0.188 | 0.004 | 0.203 | |
| Quickload-class | 0.464 | 0.032 | 1.586 | |
| QuickloadGenome-class | 0.240 | 0.004 | 0.258 | |
| TwoBitFile-class | 0.080 | 0.000 | 0.081 | |
| UCSCSchema-class | 0.000 | 0.000 | 0.001 | |
| UCSCTableQuery-class | 0.004 | 0.000 | 0.002 | |
| WIGFile-class | 0.876 | 0.008 | 0.888 | |
| asBED | 0 | 0 | 0 | |
| asGFF | 0.004 | 0.000 | 0.001 | |
| browseGenome | 0.000 | 0.000 | 0.001 | |
| browserView-methods | 0.004 | 0.000 | 0.001 | |
| browserViews-methods | 0.000 | 0.000 | 0.001 | |
| cpneTrack | 0.500 | 0.012 | 0.510 | |
| export | 0.060 | 0.000 | 0.067 | |
| layTrack-methods | 0.000 | 0.000 | 0.001 | |
| liftOver | 0 | 0 | 0 | |
| readGFF | 0.388 | 0.004 | 0.394 | |
| targets | 0.068 | 0.000 | 0.069 | |
| ucscGenomes | 0.152 | 0.004 | 0.679 | |
| ucscTrackModes-methods | 0.020 | 0.000 | 0.019 | |