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 '/loc/home/biocbuild/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* 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 ... 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 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 was 1 warning, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck/00check.log
for details
* Installing *source* package 'BiostringsCinterfaceDemo' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c read_fasta_demo12.c -o read_fasta_demo12.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c read_fasta_demo3.c -o read_fasta_demo3.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c R_init_BiostringsCinterfaceDemo.c -o R_init_BiostringsCinterfaceDemo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c test.c -o test.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/local/lib -o BiostringsCinterfaceDemo.so alphabet_by_cycle.o Biostrings_stubs.o read_fasta_demo12.o read_fasta_demo3.o read_solexa_sequence.o R_init_BiostringsCinterfaceDemo.o test.o utils.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** help
>>> Building/Updating help pages for package 'BiostringsCinterfaceDemo'
Formats: text html latex example
SolexaSequenceQ-class text html latex example
alphabetByCycle text html latex example
read.fasta.demo text html latex example
readSolexaQ text html latex example
utilities text html latex example
** building package indices ...
* DONE (BiostringsCinterfaceDemo)