prism 0.1.2
Raphael Gottardo
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/prism | | Last Changed Rev: 30615 / Revision: 30951 | | Last Changed Date: 2008-03-21 12:42:17 -0700 (Fri, 21 Mar 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/prism.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* checking for file 'prism/DESCRIPTION' ... OK
* this is package 'prism' 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 'prism' can be installed ... WARNING
Found the following significant warnings:
util.c:871: warning: 'J' is used uninitialized in this function
util.c:880: warning: 'K' is used uninitialized in this function
See 'E:/biocbld/bbs-2.2-bioc/meat/prism.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 ... 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 using pdflatex ... OK
WARNING: There were 3 warnings, see
E:/biocbld/bbs-2.2-bioc/meat/prism.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.2-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 -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c bisegment.c -o bisegment.o
bisegment.c: In function 'R_link_bisegment':
bisegment.c:144: warning: unused variable 'gamma_start'
bisegment.c:136: warning: unused variable 'bj'
bisegment.c:136: warning: unused variable 'bi'
bisegment.c: In function 'bisegment':
bisegment.c:326: warning: unused variable 'j_end'
bisegment.c:326: warning: unused variable 'j_start'
bisegment.c:325: warning: unused variable 'i_end'
bisegment.c:325: warning: unused variable 'i_start'
bisegment.c:321: warning: unused variable 'stop_criteria_M'
bisegment.c:314: warning: unused variable 'l'
bisegment.c:314: warning: unused variable 'jjj'
bisegment.c:314: warning: unused variable 'iii'
bisegment.c:314: warning: unused variable 'kk'
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:874: warning: unused variable 'sum_res'
bisegment.c:873: warning: unused variable 'nb_pixel'
bisegment.c: In function 'compute_difference':
bisegment.c:887: warning: unused variable 'i'
bisegment.c: In function 'compute_uncertainty':
bisegment.c:904: warning: unused variable 'nb_flagged'
bisegment.c:901: warning: unused variable 'jjj'
bisegment.c:901: warning: unused variable 'iii'
bisegment.c: In function 'bisegment_mcmc':
bisegment.c:1000: warning: unused variable 'nb_pix'
bisegment.c:991: warning: unused variable 'rho_new'
bisegment.c:990: warning: unused variable 'log_like_rho_new'
bisegment.c:989: warning: unused variable 'log_like_rho'
bisegment.c:988: warning: unused variable 'nb_spot'
bisegment.c:982: warning: unused variable 'l'
bisegment.c:982: warning: unused variable 'jjj'
bisegment.c:982: warning: unused variable 'iii'
bisegment.c:981: warning: unused variable 'countrho'
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 &
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c find_grid.c -o find_grid.o
find_grid.c: In function 'find_grid':
find_grid.c:12: warning: 'index_min' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -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:871: warning: 'J' is used uninitialized in this function
util.c:880: warning: 'K' is used uninitialized in this function
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i prism_res.rc -o prism_res.o
gcc -std=gnu99 -shared -s -o prism.dll prism.def bisegment.o find_grid.o util.o prism_res.o -Le:/biocbld/bbs-2.2-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-2.2-bioc\meat\prism.Rcheck\00_pkg_src\prism\chm\prism.chm
Compile time: 0 minutes, 1 second
10 Topics
53 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\prism.Rcheck\00_pkg_src\prism\chm\prism.chm, 28,130 bytes
Compression decreased file by 15,233 bytes.
adding MD5 sums
* DONE (prism)