Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

Package 443/516HostnameOS / ArchBUILDCHECKBUILD BIN
rtracklayer 1.14.4
Michael Lawrence
Snapshot Date: 2012-01-06 18:22:10 -0800 (Fri, 06 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/rtracklayer
Last Changed Rev: 60820 / Revision: 61878
Last Changed Date: 2011-11-23 08:02:43 -0800 (Wed, 23 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: rtracklayer
Version: 1.14.4
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch rtracklayer_1.14.4.tar.gz
StartedAt: 2012-01-07 04:47:46 -0800 (Sat, 07 Jan 2012)
EndedAt: 2012-01-07 04:51:04 -0800 (Sat, 07 Jan 2012)
EllapsedTime: 197.4 seconds
RetCode: 0
Status:  OK  
CheckDir: rtracklayer.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/rtracklayer.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.14.4'
* 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 whether package 'rtracklayer' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  cpneTrack.rda    769Kb    591Kb       xz
  targets.rda      147Kb     61Kb       xz
* 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 ... NOTE
File 'E:/biocbld/bbs-2.9-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs/i386/rtracklayer.dll':
  Found '_assert', possibly from 'assert' (C)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... 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

rtracklayer.Rcheck/00install.out:

* installing *source* package 'rtracklayer' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:222:32: warning: 'ans_score' may be used uninitialized in this function
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -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  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
twoBit.c: In function 'TwoBitFile_read':
twoBit.c:110:35: warning: pointer targets in passing argument 3 of 'Ocopy_bytes_to_i1i2_with_lkup' differ in signedness
E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include/IRanges_interface.h:342:6: note: expected 'char *' but argument is of type 'Rbyte *'
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:590:1: warning: implicit declaration of function 'bzero'
ucsc/bbiRead.c:590:1: warning: incompatible implicit declaration of built-in function 'bzero'
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:234:1: warning: too many arguments for format
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:315:5: warning: too many arguments for format
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:330:9: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
ucsc/cirTree.c:330:9: warning: format '%s' expects type 'char *', but argument 3 has type 'long long unsigned int'
ucsc/cirTree.c:330:9: warning: too many arguments for format
ucsc/cirTree.c: At top level:
ucsc/cirTree.c:454:8: warning: return type defaults to 'int'
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:497:1: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:497:1: warning: format '%u' expects type 'unsigned int', but argument 3 has type 'long long unsigned int'
ucsc/cirTree.c:497:1: warning: too many arguments for format
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2370:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:2370:5: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/common.c:2370:5: warning: too many arguments for format
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2381:2: warning: unknown conversion type character 'l' in format
ucsc/common.c:2381:2: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/common.c:2381:2: warning: too many arguments for format
ucsc/common.c:2383:2: warning: unknown conversion type character 'l' in format
ucsc/common.c:2383:2: warning: too many arguments for format
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2521:2: warning: unknown conversion type character 'l' in format
ucsc/common.c:2521:2: warning: too many arguments for format
ucsc/common.c:2523:2: warning: unknown conversion type character 'l' in format
ucsc/common.c:2523:2: warning: unknown conversion type character 'l' in format
ucsc/common.c:2523:2: warning: too many arguments for format
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2543:3: warning: unknown conversion type character 'l' in format
ucsc/common.c:2543:3: warning: format '%s' expects type 'char *', but argument 3 has type 'long long int'
ucsc/common.c:2543:3: warning: format '%d' expects type 'int', but argument 4 has type 'char *'
ucsc/common.c:2543:3: warning: too many arguments for format
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2668:9: warning: unknown conversion type character 'l' in format
ucsc/common.c:2668:9: warning: unknown conversion type character 'l' in format
ucsc/common.c:2668:9: warning: too many arguments for format
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3134:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3134:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3134:5: warning: too many arguments for format
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3143:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3143:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3143:5: warning: too many arguments for format
ucsc/common.c: In function 'safecat':
ucsc/common.c:3157:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3157:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3157:5: warning: too many arguments for format
ucsc/common.c: In function 'safencat':
ucsc/common.c:3166:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3166:5: warning: unknown conversion type character 'l' in format
ucsc/common.c:3166:5: warning: too many arguments for format
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds
ucsc/common.c:2766:21: warning: array subscript is above array bounds
ucsc/common.c:2767:21: warning: array subscript is above array bounds
ucsc/common.c:2768:21: warning: array subscript is above array bounds
ucsc/common.c:2769:8: warning: array subscript is above array bounds
ucsc/common.c:2770:8: warning: array subscript is above array bounds
ucsc/common.c:2771:8: warning: array subscript is above array bounds
ucsc/common.c:2772:8: warning: array subscript is above array bounds
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds
ucsc/common.c:2766:21: warning: array subscript is above array bounds
ucsc/common.c:2767:21: warning: array subscript is above array bounds
ucsc/common.c:2768:21: warning: array subscript is above array bounds
ucsc/common.c:2769:8: warning: array subscript is above array bounds
ucsc/common.c:2770:8: warning: array subscript is above array bounds
ucsc/common.c:2771:8: warning: array subscript is above array bounds
ucsc/common.c:2772:8: warning: array subscript is above array bounds
ucsc/common.c: In function 'fdReadBits64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds
ucsc/common.c:2766:21: warning: array subscript is above array bounds
ucsc/common.c:2767:21: warning: array subscript is above array bounds
ucsc/common.c:2768:21: warning: array subscript is above array bounds
ucsc/common.c:2769:8: warning: array subscript is above array bounds
ucsc/common.c:2770:8: warning: array subscript is above array bounds
ucsc/common.c:2771:8: warning: array subscript is above array bounds
ucsc/common.c:2772:8: warning: array subscript is above array bounds
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds
ucsc/common.c:2766:21: warning: array subscript is above array bounds
ucsc/common.c:2767:21: warning: array subscript is above array bounds
ucsc/common.c:2768:21: warning: array subscript is above array bounds
ucsc/common.c:2769:8: warning: array subscript is above array bounds
ucsc/common.c:2770:8: warning: array subscript is above array bounds
ucsc/common.c:2771:8: warning: array subscript is above array bounds
ucsc/common.c:2772:8: warning: array subscript is above array bounds
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2899:21: warning: array subscript is above array bounds
ucsc/common.c:2900:21: warning: array subscript is above array bounds
ucsc/common.c:2901:21: warning: array subscript is above array bounds
ucsc/common.c:2902:21: warning: array subscript is above array bounds
ucsc/common.c:2903:8: warning: array subscript is above array bounds
ucsc/common.c:2904:8: warning: array subscript is above array bounds
ucsc/common.c:2905:8: warning: array subscript is above array bounds
ucsc/common.c:2906:8: warning: array subscript is above array bounds
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2899:21: warning: array subscript is above array bounds
ucsc/common.c:2900:21: warning: array subscript is above array bounds
ucsc/common.c:2901:21: warning: array subscript is above array bounds
ucsc/common.c:2902:21: warning: array subscript is above array bounds
ucsc/common.c:2903:8: warning: array subscript is above array bounds
ucsc/common.c:2904:8: warning: array subscript is above array bounds
ucsc/common.c:2905:8: warning: array subscript is above array bounds
ucsc/common.c:2906:8: warning: array subscript is above array bounds
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2899:21: warning: array subscript is above array bounds
ucsc/common.c:2900:21: warning: array subscript is above array bounds
ucsc/common.c:2901:21: warning: array subscript is above array bounds
ucsc/common.c:2902:21: warning: array subscript is above array bounds
ucsc/common.c:2903:8: warning: array subscript is above array bounds
ucsc/common.c:2904:8: warning: array subscript is above array bounds
ucsc/common.c:2905:8: warning: array subscript is above array bounds
ucsc/common.c:2906:8: warning: array subscript is above array bounds
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:39:5: warning: unknown conversion type character 'l' in format
ucsc/localmem.c:39:5: warning: too many arguments for format
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:49:6: warning: unknown conversion type character 'l' in format
ucsc/zlibFace.c:49:6: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/zlibFace.c:49:6: warning: too many arguments for format
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:70:6: warning: unknown conversion type character 'l' in format
ucsc/zlibFace.c:70:6: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/zlibFace.c:70:6: warning: too many arguments for format
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:469:21: warning: 'e' may be used uninitialized in this function
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:91:10: warning: too many arguments for format
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:94:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
ucsc/memalloc.c:94:14: warning: too many arguments for format
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:114:10: warning: too many arguments for format
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:117:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
ucsc/memalloc.c:117:14: warning: too many arguments for format
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:139:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
ucsc/memalloc.c:139:14: warning: too many arguments for format
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:161:2: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
ucsc/memalloc.c:161:2: warning: too many arguments for format
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:187:10: warning: too many arguments for format
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:190:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
ucsc/memalloc.c:190:14: warning: too many arguments for format
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:318:14: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:318:14: warning: too many arguments for format
ucsc/memalloc.c:322:14: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:322:14: warning: too many arguments for format
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:360:18: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:360:18: warning: too many arguments for format
ucsc/memalloc.c:364:18: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:364:18: warning: too many arguments for format
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:133:2: warning: unknown conversion type character 'l' in format
ucsc/udc.c:133:2: warning: too many arguments for format
ucsc/udc.c:138:5: warning: unknown conversion type character 'l' in format
ucsc/udc.c:138:5: warning: unknown conversion type character 'l' in format
ucsc/udc.c:138:5: warning: too many arguments for format
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:229:1: warning: unknown conversion type character 'l' in format
ucsc/udc.c:229:1: warning: format '%s' expects type 'char *', but argument 4 has type 'long long unsigned int'
ucsc/udc.c:229:1: warning: too many arguments for format
ucsc/udc.c:236:5: warning: unknown conversion type character 'l' in format
ucsc/udc.c:236:5: warning: too many arguments for format
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:285:1: warning: unknown conversion type character 'l' in format
ucsc/udc.c:285:1: warning: format '%s' expects type 'char *', but argument 4 has type 'long long unsigned int'
ucsc/udc.c:285:1: warning: too many arguments for format
ucsc/udc.c:303:2: warning: unknown conversion type character 'l' in format
ucsc/udc.c:303:2: warning: too many arguments for format
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:495:7: warning: unknown conversion type character 'l' in format
ucsc/udc.c:495:7: warning: format '%d' expects type 'int', but argument 4 has type 'long long int'
ucsc/udc.c:495:7: warning: too many arguments for format
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format
ucsc/udc.c:644:3: warning: format '%s' expects type 'char *', but argument 3 has type 'long long unsigned int'
ucsc/udc.c:644:3: warning: format '%d' expects type 'int', but argument 4 has type 'long long int'
ucsc/udc.c:644:3: warning: too many arguments for format
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1086:3: warning: unknown conversion type character 'l' in format
ucsc/udc.c:1086:3: warning: unknown conversion type character 'l' in format
ucsc/udc.c:1086:3: warning: too many arguments for format
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1110:4: warning: unknown conversion type character 'l' in format
ucsc/udc.c:1110:4: warning: format '%s' expects type 'char *', but argument 2 has type 'long long unsigned int'
ucsc/udc.c:1110:4: warning: unknown conversion type character 'l' in format
ucsc/udc.c:1110:4: warning: format '%d' expects type 'int', but argument 3 has type 'char *'
ucsc/udc.c:1110:4: warning: too many arguments for format
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1436:6: warning: unknown conversion type character 'l' in format
ucsc/udc.c:1436:6: warning: unknown conversion type character 'l' in format
ucsc/udc.c:1436:6: warning: too many arguments for format
ucsc/udc.c: At top level:
ucsc/udc.c:121:13: warning: 'readAndIgnore' defined but not used
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def IRanges_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.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 -LE:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs/i386
** 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'
Creating a generic function for 'toString' from package 'base' in package 'rtracklayer'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'rtracklayer.Rnw' 
** testing if installed package can be loaded

* DONE (rtracklayer)

rtracklayer.Rcheck/rtracklayer-Ex.timings:

nameusersystemelapsed
BigWigFile2.480.092.63
BigWigSelection-class0.020.020.03
GenomicSelection 0.34 0.1712.25
Quickload-class0.020.000.05
QuickloadGenome-class0.140.000.21
RangedData-methods0.480.000.49
TwoBitFile-class0.140.000.14
UCSCSchema-class000
UCSCTableQuery-class0.020.000.02
asBED000
browseGenome000
browserView-methods000
browserViews-methods000
cpneTrack0.620.020.64
export0.110.000.11
export.gff0.910.031.01
import0.110.000.44
import.gff0.270.010.28
layTrack-methods000
liftOver000
targets0.040.000.05
ucscGenomes0.080.020.29
ucscTrackModes-methods000