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Package 43/264HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: BiostringsCinterfaceDemo
Version: 0.1.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check BiostringsCinterfaceDemo_0.1.2.tar.gz
StartedAt: 2008-04-09 05:04:59 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 05:05:42 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 43.5 seconds
RetCode: 0
Status: WARNINGS
CheckDir: BiostringsCinterfaceDemo.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ASCII
* 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
  /Users/biocbuild/bbs-2.2-bioc/meat/BiostringsCinterfaceDemo.Rcheck/00check.log
for details

BiostringsCinterfaceDemo.Rcheck/00install.out:

* Installing *source* package 'BiostringsCinterfaceDemo' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -Wall -c R_init_BiostringsCinterfaceDemo.c -o R_init_BiostringsCinterfaceDemo.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -Wall -c read_fasta_demo12.c -o read_fasta_demo12.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -Wall -c read_fasta_demo3.c -o read_fasta_demo3.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -Wall -c test.c -o test.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -march=nocona -Wall -c utils.c -o utils.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BiostringsCinterfaceDemo.so 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   -F/Library/Frameworks/R.framework/.. -framework R -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c R_init_BiostringsCinterfaceDemo.c -o R_init_BiostringsCinterfaceDemo.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/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-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c read_fasta_demo12.c -o read_fasta_demo12.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c read_fasta_demo3.c -o read_fasta_demo3.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/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-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c test.c -o test.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c utils.c -o utils.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BiostringsCinterfaceDemo.so 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   -F/Library/Frameworks/R.framework/.. -framework R -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c R_init_BiostringsCinterfaceDemo.c -o R_init_BiostringsCinterfaceDemo.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c read_fasta_demo12.c -o read_fasta_demo12.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c read_fasta_demo3.c -o read_fasta_demo3.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c test.c -o test.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c utils.c -o utils.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BiostringsCinterfaceDemo.so 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   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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)