rtracklayer 1.13.0
Michael Lawrence
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rtracklayer | | Last Changed Rev: 55209 / Revision: 55359 | | Last Changed Date: 2011-05-03 05:40:27 -0700 (Tue, 03 May 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/rtracklayer.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.13.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘rtracklayer’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘IRanges’
All user-level objects in a package should have documentation entries.
See the 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 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ calls not declared from:
‘GGtools’ ‘hgu133plus2.db’
* 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 was 1 warning, see
‘/loc/home/biocbuild/bbs-2.9-bioc/meat/rtracklayer.Rcheck/00check.log’
for details
* installing *source* package ‘rtracklayer’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for off_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uid_t in sys/types.h... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking whether time.h and sys/time.h may both be included... yes
checking for sys/time.h... (cached) yes
checking for unistd.h... (cached) yes
checking for alarm... yes
checking for working mktime... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for bzero... yes
checking for dup2... yes
checking for getcwd... yes
checking for gethostbyname... yes
checking for gettimeofday... yes
checking for memmove... yes
checking for memset... yes
checking for mkdir... yes
checking for regcomp... yes
checking for select... yes
checking for socket... yes
checking for sqrt... no
checking for strcasecmp... yes
checking for strchr... yes
checking for strcspn... yes
checking for strdup... yes
checking for strerror... yes
checking for strrchr... yes
checking for strspn... yes
checking for strstr... yes
checking for uname... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:189:32: warning: ‘ans_score’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c chain_io.c -o chain_io.o
chain_io.c: In function ‘read_chain_file’:
chain_io.c:34:7: warning: ‘tstart’ may be used uninitialized in this function
chain_io.c:34:15: warning: ‘qstart’ may be used uninitialized in this function
chain_io.c:35:48: warning: ‘trc’ may be used uninitialized in this function
chain_io.c:35:53: warning: ‘qrc’ may be used uninitialized in this function
chain_io.c:36:15: warning: ‘block’ may be used uninitialized in this function
chain_io.c:39:24: warning: ‘header_line’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘byteSwap64’:
ucsc/common.c:2169:21: warning: array subscript is above array bounds
ucsc/common.c:2170:21: warning: array subscript is above array bounds
ucsc/common.c:2171:21: warning: array subscript is above array bounds
ucsc/common.c:2172:21: warning: array subscript is above array bounds
ucsc/common.c:2173:8: warning: array subscript is above array bounds
ucsc/common.c:2174:8: warning: array subscript is above array bounds
ucsc/common.c:2175:8: warning: array subscript is above array bounds
ucsc/common.c:2176:8: warning: array subscript is above array bounds
ucsc/common.c: In function ‘byteSwapDouble’:
ucsc/common.c:2273:21: warning: array subscript is above array bounds
ucsc/common.c:2274:21: warning: array subscript is above array bounds
ucsc/common.c:2275:21: warning: array subscript is above array bounds
ucsc/common.c:2276:21: warning: array subscript is above array bounds
ucsc/common.c:2277:8: warning: array subscript is above array bounds
ucsc/common.c:2278:8: warning: array subscript is above array bounds
ucsc/common.c:2279:8: warning: array subscript is above array bounds
ucsc/common.c:2280:8: warning: array subscript is above array bounds
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/errabort.c -o ucsc/errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcInfoViaHttp’:
ucsc/udc.c:355:1: warning: implicit declaration of function ‘strptime’
ucsc/udc.c:355:62: warning: comparison between pointer and integer
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -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 ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.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/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: bitops
Creating a new generic function for "nrow" in "rtracklayer"
Creating a new generic function for "offset" in "rtracklayer"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘rtracklayer.Rnw’
** testing if installed package can be loaded
* DONE (rtracklayer)