BiostringsCinterfaceDemo 0.1.2
H. Pages
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiostringsCinterfaceDemo | | Last Changed Rev: 30788 / Revision: 30951 | | Last Changed Date: 2008-04-01 16:41:29 -0700 (Tue, 01 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* checking for file 'BiostringsCinterfaceDemo/DESCRIPTION' ... OK
* this is package 'BiostringsCinterfaceDemo' version '0.1.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BiostringsCinterfaceDemo' can be installed ... WARNING
Found the following significant warnings:
missing link(s): DNAStringSet-class BStringSet-class
missing link(s): DNAStringSet-class
See 'E:/biocbld/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck/00install.out' for details.
* 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
SolexaSequenceQ
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating BiostringsCinterfaceDemo-Ex.R ... OK
* checking examples ... OK
* creating BiostringsCinterfaceDemo-manual.tex ... OK
* checking BiostringsCinterfaceDemo-manual.tex using pdflatex ... OK
WARNING: There were 2 warnings, see
E:/biocbld/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck
---------- Making package BiostringsCinterfaceDemo ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making Biostrings_stubs.d from Biostrings_stubs.c
making R_init_BiostringsCinterfaceDemo.d from R_init_BiostringsCinterfaceDemo.c
making alphabet_by_cycle.d from alphabet_by_cycle.c
making read_fasta_demo12.d from read_fasta_demo12.c
making read_fasta_demo3.d from read_fasta_demo3.c
making read_solexa_sequence.d from read_solexa_sequence.c
making test.d from test.c
making utils.d from utils.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c R_init_BiostringsCinterfaceDemo.c -o R_init_BiostringsCinterfaceDemo.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c alphabet_by_cycle.c -o alphabet_by_cycle.o
alphabet_by_cycle.c: In function 'alphabet_by_cycle':
alphabet_by_cycle.c:51: warning: 'decode' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c read_fasta_demo12.c -o read_fasta_demo12.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c read_fasta_demo3.c -o read_fasta_demo3.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c read_solexa_sequence.c -o read_solexa_sequence.o
read_solexa_sequence.c: In function 'read_solexa_fasta':
read_solexa_sequence.c:186: warning: unused variable 'nms'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c test.c -o test.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/Biostrings/include" -O3 -Wall -c utils.c -o utils.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i BiostringsCinterfaceDemo_res.rc -o BiostringsCinterfaceDemo_res.o
gcc -std=gnu99 -shared -s -o BiostringsCinterfaceDemo.dll BiostringsCinterfaceDemo.def Biostrings_stubs.o R_init_BiostringsCinterfaceDemo.o alphabet_by_cycle.o read_fasta_demo12.o read_fasta_demo3.o read_solexa_sequence.o test.o utils.o BiostringsCinterfaceDemo_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'BiostringsCinterfaceDemo'
Formats: text html latex example chm
SolexaSequenceQ-class text html latex example chm
missing link(s): DNAStringSet-class BStringSet-class
alphabetByCycle text html latex example chm
missing link(s): DNAStringSet-class
read.fasta.demo text html latex example chm
readSolexaQ text html latex example chm
utilities text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\BiostringsCinterfaceDemo.Rcheck\00_pkg_src\BiostringsCinterfaceDemo\chm\BiostringsCinterfaceDemo.chm
Compile time: 0 minutes, 0 seconds
6 Topics
24 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\BiostringsCinterfaceDemo.Rcheck\00_pkg_src\BiostringsCinterfaceDemo\chm\BiostringsCinterfaceDemo.chm, 23,525 bytes
Compression decreased file by 3,143 bytes.
adding MD5 sums
* DONE (BiostringsCinterfaceDemo)