Package: prism

Version: 0.1.1

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check prism_0.1.1.tar.gz

RetCode: 0

Time: 46.5 seconds

Status: WARNINGS

CheckDir: prism.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/prism.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'prism/DESCRIPTION' ... OK
* this is package 'prism' version '0.1.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'prism' 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  methods
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGrid: no visible global function definition for 'scale.image'
prism: no visible binding for global variable 'phi1.block'
prism: no visible binding for global variable 'phi2.block'
* 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 'prismEstimates':
prism
  Code: function(I, B = 1000, grid, print = FALSE, mcmc = FALSE)
  Docs: function()
  Argument names in code not in docs:
    I B grid print mcmc

Codoc mismatches from documentation object 'prismGrid':
getGrid
  Code: function(I, blocks.nb, spots.nb, radius, retouch = FALSE,
                 scaling.factor = 2)
  Docs: function()
  Argument names in code not in docs:
    I blocks.nb spots.nb radius retouch scaling.factor

Codoc mismatches from documentation object 'prismImage':
formImagePair
  Code: function(file1, file2, reverse = FALSE, factor = 1)
  Docs: function()
  Argument names in code not in docs:
    file1 file2 reverse factor

* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... 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 prism-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating prism-manual.tex ... OK
* checking prism-manual.tex ... OK

WARNING: There were 2 warnings, see
  E:/biocbld/bbs-2.1-bioc/meat/prism.Rcheck/00check.log
for details

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/prism.Rcheck


---------- Making package prism ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making bisegment.d from bisegment.c
making find_grid.d from find_grid.c
making util.d from util.c
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c bisegment.c -o bisegment.o
bisegment.c: In function `R_link_bisegment':
bisegment.c:136: warning: unused variable `bi'
bisegment.c:136: warning: unused variable `bj'
bisegment.c:144: warning: unused variable `gamma_start'
bisegment.c: In function `bisegment':
bisegment.c:314: warning: unused variable `kk'
bisegment.c:314: warning: unused variable `iii'
bisegment.c:314: warning: unused variable `jjj'
bisegment.c:314: warning: unused variable `l'
bisegment.c:321: warning: unused variable `stop_criteria_M'
bisegment.c:325: warning: unused variable `i_start'
bisegment.c:325: warning: unused variable `i_end'
bisegment.c:326: warning: unused variable `j_start'
bisegment.c:326: warning: unused variable `j_end'
bisegment.c:460: warning: no return statement in function returning non-void
bisegment.c: In function `initialize_image':
bisegment.c:633: warning: suggest parentheses around comparison in operand of &
bisegment.c: In function `up_date_beta_mrf':
bisegment.c:780: warning: suggest parentheses around comparison in operand of &
bisegment.c:780: warning: suggest parentheses around comparison in operand of &
bisegment.c:780: warning: suggest parentheses around comparison in operand of &
bisegment.c:781: warning: suggest parentheses around comparison in operand of &
bisegment.c:784: warning: suggest parentheses around comparison in operand of &
bisegment.c:789: warning: suggest parentheses around comparison in operand of &
bisegment.c:794: warning: suggest parentheses around comparison in operand of &
bisegment.c: In function `up_date_w':
bisegment.c:873: warning: unused variable `nb_pixel'
bisegment.c:874: warning: unused variable `sum_res'
bisegment.c: In function `compute_difference':
bisegment.c:887: warning: unused variable `i'
bisegment.c: In function `compute_uncertainty':
bisegment.c:901: warning: unused variable `iii'
bisegment.c:901: warning: unused variable `jjj'
bisegment.c:904: warning: unused variable `nb_flagged'
bisegment.c: In function `bisegment_mcmc':
bisegment.c:981: warning: unused variable `countrho'
bisegment.c:982: warning: unused variable `iii'
bisegment.c:982: warning: unused variable `jjj'
bisegment.c:982: warning: unused variable `l'
bisegment.c:988: warning: unused variable `nb_spot'
bisegment.c:989: warning: unused variable `log_like_rho'
bisegment.c:990: warning: unused variable `log_like_rho_new'
bisegment.c:991: warning: unused variable `rho_new'
bisegment.c:1000: warning: unused variable `nb_pix'
bisegment.c:1285: warning: no return statement in function returning non-void
bisegment.c: In function `slice_sampling_lambda_eps':
bisegment.c:1830: warning: suggest parentheses around comparison in operand of &
bisegment.c:1839: warning: suggest parentheses around comparison in operand of &
bisegment.c: In function `change_resolution_mcmc':
bisegment.c:2120: warning: suggest parentheses around comparison in operand of &
bisegment.c:2122: warning: suggest parentheses around comparison in operand of &
bisegment.c:2124: warning: suggest parentheses around comparison in operand of &
bisegment.c: In function `bisegment':
bisegment.c:460: warning: control reaches end of non-void function
bisegment.c: In function `bisegment_mcmc':
bisegment.c:1285: warning: control reaches end of non-void function
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c find_grid.c -o find_grid.o
find_grid.c: In function `find_grid':
find_grid.c:12: warning: 'index_min' might be used uninitialized in this function
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c util.c -o util.o
util.c: In function `qr_solve':
util.c:623: warning: implicit declaration of function `dqrdc2_'
util.c:638: warning: implicit declaration of function `dqrcf_'
util.c:602: warning: unused variable `vmax'
util.c: In function `inverse':
util.c:661: warning: unused variable `j'
util.c: In function `product_mat_vec':
util.c:708: warning: unused variable `k'
util.c: In function `slice_sampling_phi':
util.c:816: warning: suggest parentheses around comparison in operand of &
util.c:824: warning: suggest parentheses around comparison in operand of &
util.c:798: warning: unused variable `v'
util.c: In function `slice_sampling_lxi':
util.c:871: warning: suggest parentheses around comparison in operand of &
util.c:880: warning: suggest parentheses around comparison in operand of &
util.c: In function `slice_sampling_lambda':
util.c:943: warning: suggest parentheses around comparison in operand of &
util.c:952: warning: suggest parentheses around comparison in operand of &
util.c: In function `slice_sampling_b':
util.c:1008: warning: suggest parentheses around comparison in operand of &
util.c:1016: warning: suggest parentheses around comparison in operand of &
util.c: In function `slice_sampling_a':
util.c:1063: warning: suggest parentheses around comparison in operand of &
util.c:1071: warning: suggest parentheses around comparison in operand of &
util.c: In function `slice_sampling_lxi':
util.c:856: warning: 'J' might be used uninitialized in this function
util.c:856: warning: 'K' might be used uninitialized in this function
windres -I e:/biocbld/bbs-2.1-bioc/R/include  -i prism_res.rc -o prism_res.o
gcc  -shared -s  -o prism.dll prism.def bisegment.o find_grid.o util.o prism_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package prism for lazy loading
Loading required package: EBImage
Creating a new generic function for "summary" in "prism"
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'prism'
     Formats: text html latex example chm 
  extractExpression                 text    html    latex   example chm
  formImagePair                     text    html    latex   example chm
  getGrid                           text    html    latex   example chm
  like                              text    html    latex           chm
  plotEstimates                     text    html    latex   example chm
  prism                             text    html    latex   example chm
  prismEstimates-class              text    html    latex   example chm
  prismGrid-class                   text    html    latex   example chm
  prismImage-class                  text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\prism.Rcheck\00_pkg_src\prism\chm\prism.chm


Compile time: 0 minutes, 0 seconds
10	Topics
53	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\prism.Rcheck\00_pkg_src\prism\chm\prism.chm, 28,120 bytes
Compression decreased file by 15,231 bytes.
  adding MD5 sums

* DONE (prism)