rtracklayer 1.8.1
Michael Lawrence
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/rtracklayer | | Last Changed Rev: 48426 / Revision: 49923 | | Last Changed Date: 2010-07-26 11:43:59 -0700 (Mon, 26 Jul 2010) |
| wilson1 | Linux (openSUSE 11.1) / 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 |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/rtracklayer.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.8.1'
* 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 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 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 RangedDataList
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking data for non-ASCII characters ... 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
E:/biocbld/bbs-2.6-bioc/meat/rtracklayer.Rcheck/00check.log
for details
* install options are ' --no-html'
* installing *source* package 'rtracklayer' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:189: warning: 'ans_score' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:552: warning: implicit declaration of function 'bzero'
ucsc/bbiRead.c:552: warning: incompatible implicit declaration of built-in function 'bzero'
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/common.c -o ucsc/common.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/hash.c -o ucsc/hash.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:37: warning: 'getDecompressor' defined but not used
ucsc/linefile.c:105: warning: 'headerBytes' defined but not used
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:469: warning: 'e' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/udc.c -o ucsc/udc.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/net.c -o ucsc/net.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/bits.c -o ucsc/bits.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/internet.c -o ucsc/internet.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/https.c -o ucsc/https.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/base64.c -o ucsc/base64.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/os.c -o ucsc/os.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -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 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 -lRzlib -lws2_32 -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs
... done
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: bitops
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (rtracklayer)