rtracklayer 1.19.6
Michael Lawrence
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rtracklayer | | Last Changed Rev: 72400 / Revision: 72575 | | Last Changed Date: 2013-01-09 10:16:38 -0800 (Wed, 09 Jan 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/rtracklayer.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.19.6’
* 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 DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
decompress,CompressedFile: no visible global function definition for
‘manageConnection’
sortBySeqnameAndStart,RangesList: no visible binding for global
variable ‘value’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'track<-' and siglist 'UCSCSession,RTLFile'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'browseGenome':
\S4method{browseGenome}{GRanges}
Code: function(object, ...)
Docs: function(object, browser = "UCSC", range = base::range(object),
view = TRUE, trackParams = list(), viewParams =
list(), name = "customTrack", ...)
Argument names in docs not in code:
browser range view trackParams viewParams name
Mismatches in argument names:
Position: 2 Code: ... Docs: browser
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs/rtracklayer.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Object: ‘ucsc/errabort.o’
Found ‘exit’, possibly from ‘exit’ (C)
Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’
Found ‘printf’, possibly from ‘printf’ (C)
Objects: ‘ucsc/pipeline.o’, ‘ucsc/net.o’
Found ‘putchar’, possibly from ‘putchar’ (C)
Object: ‘ucsc/net.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Object: ‘ucsc/pipeline.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Objects: ‘ucsc/errabort.o’, ‘ucsc/obscure.o’, ‘ucsc/net.o’,
‘ucsc/verbose.o’, ‘ucsc/os.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/net.o’,
‘ucsc/verbose.o’, ‘ucsc/os.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BigWigFile 5.433 1.172 6.616
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 3 warnings.
NOTE: There was 1 note.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
* installing *source* package ‘rtracklayer’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c chain_io.c -o chain_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c handlers.c -o handlers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcInfoViaHttp’:
ucsc/udc.c:405:1: warning: implicit declaration of function ‘strptime’
ucsc/udc.c:405:62: warning: comparison between pointer and integer
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/net.c -o ucsc/net.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -g -fpic -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o rtracklayer.so IRanges_stubs.o R_init_rtracklayer.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 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
‘rtracklayer.Rnw’
** testing if installed package can be loaded
* DONE (rtracklayer)