Rsamtools 1.0.8
Biocore Team c/o BioC user list
| 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/Rsamtools | | Last Changed Rev: 48803 / Revision: 49923 | | Last Changed Date: 2010-08-13 15:05:51 -0700 (Fri, 13 Aug 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ OK ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/Rsamtools.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsamtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsamtools' version '1.0.8'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rsamtools' 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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 tests ...
Running 'runalltests.R'
Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...18a19,21
> [bam_index_load] fail to load BAM index.
> [bam_index_load] fail to load BAM index.
> open: No such file or directory
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package 'Rsamtools' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c io_sam.c -o io_sam.o
In file included from D:/biocbld/bbs-2.6-bioc/R/include/Rdefines.h:26,
from D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include/IRanges_interface.h:12,
from io_sam.c:5:
D:/biocbld/bbs-2.6-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/windows.h:64,
from c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/winsock2.h:16,
from samtools/knetfile.h:12,
from samtools/bgzf.h:32,
from samtools/bam.h:50,
from samtools/sam.h:4,
from io_sam.c:1:
c:/rtools211/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:1: warning: this is the location of the previous definition
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c utilities.c -o utilities.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c encode.c -o encode.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/bam.c -o samtools/bam.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c: In function 'parse_error':
samtools/bam_import.c:166: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:166: warning: format '%s' expects type 'char *', but argument 3 has type 'int64_t'
samtools/bam_import.c:166: warning: too many arguments for format
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:179: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
samtools/bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
samtools/bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
samtools/bam_import.c: In function 'sam_read1':
samtools/bam_import.c:318: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:318: warning: too many arguments for format
samtools/bam_import.c:387: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387: warning: too many arguments for format
samtools/bam_import.c:401: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_core':
samtools/bam_index.c:177: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:177: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:177: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/kstring.c -o samtools/kstring.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/bam_aux.c -o samtools/bam_aux.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/sam_header.c -o samtools/sam_header.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/bgzf.c -o samtools/bgzf.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/razf.c -o samtools/razf.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:414: warning: unknown conversion type character 'l' in format
samtools/knetfile.c:414: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/sam.c -o samtools/sam.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -c samtools/faidx.c -o samtools/faidx.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o Rsamtools.dll tmp.def io_sam.o utilities.o encode.o Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o samtools/bam.o samtools/bam_import.o samtools/bam_index.o samtools/kstring.o samtools/bam_aux.o samtools/sam_header.o samtools/bgzf.o samtools/razf.o samtools/knetfile.o samtools/sam.o samtools/bam_pileup.o samtools/faidx.o -lRzlib -lws2_32 -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs/x64
... done
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int, table
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Rsamtools)