Package: makePlatformDesign

Version: 0.99.20

Command: /loc/biocbuild/2.0d/R/bin/R CMD check makePlatformDesign_0.99.20.tar.gz

RetCode: 0

Time: 62.7 seconds

Status: WARNINGS

CheckDir: makePlatformDesign.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/loc/biocbuild/2.0d/Rpacks/makePlatformDesign.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'makePlatformDesign/DESCRIPTION' ... OK
* this is package 'makePlatformDesign' version '0.99.20'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  oligo
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'makePlatformDesign' 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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 ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'makePDpackage':
makePDpackage
  Code: function(designFile, file1 = NULL, file2 = NULL, manufacturer =
                 c("affymetrix", "nimblegen"), type = c("expression",
                 "SNP", "tiling", "exon"), extra = NULL, genomebuild =
                 "hg12")
  Docs: function(designFile, file1 = NULL, file2 = NULL, manufacturer =
                 c("affymetrix", "nimblegen"), type = c("expression",
                 "SNP", "tiling"), extra = NULL)
  Argument names in code not in docs:
    genomebuild
  Mismatches in argument default values:
    Name: type Code: c("expression", "SNP", "tiling", "exon") Docs: c("expression", "SNP", "tiling")

* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating makePlatformDesign-Ex.R ... OK
* checking examples ... OK
* creating makePlatformDesign-manual.tex ... OK
* checking makePlatformDesign-manual.tex ... OK

WARNING: There were 2 warnings, see
  /loc/biocbuild/2.0d/Rpacks/makePlatformDesign.Rcheck/00check.log
for details

* Installing *source* package 'makePlatformDesign' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c main.c -o main.o
main.c: In function `strstr_with_pmormm':
main.c:70: warning: suggest parentheses around assignment used as truth value
main.c:87: warning: suggest parentheses around assignment used as truth value
main.c: In function `MP_matchprobes':
main.c:111: warning: `rvpos' might be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c strutils.c -o strutils.o
strutils.c:242:1: warning: "/*" within comment
strutils.c: In function `MP_longestConsecutive':
strutils.c:259: warning: int format, different type arg (arg 3)
gcc -std=gnu99 -shared -L/usr/local/lib64 -o makePlatformDesign.so main.o strutils.o   
** R
** inst
** preparing package for lazy loading
Loading required package: affyio
** help
 >>> Building/Updating help pages for package 'makePlatformDesign'
     Formats: text html latex example 
  makePDpackage                     text    html    latex   example
  makePlatformDesign-internal       text    html    latex
** building package indices ...
* DONE (makePlatformDesign)