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Package 170/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
prism0.1.1Raphael GottardoLast Changed Date: 2007-05-11 21:56:41 -0700 Last Changed Rev: 24616 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | |
wellington | Linux (SUSE 9.2) | i686 | ERROR | skipped | ||
churchill | Solaris 2.9 | sparc | OK | [ WARNINGS ] | ||
lemming | Windows Server 2003 (32-bit) | x64 | N O T S U P P O R T E D |
Package: prism |
Version: 0.1.1 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check prism_0.1.1.tar.gz |
RetCode: 0 |
Time: 96.3 seconds |
Status: WARNINGS |
CheckDir: prism.Rcheck |
Warnings: 2 |
* checking for working latex ... OK * using log directory '/loc/biocbuild/bbs-2.1-bioc/meat/prism.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-04-17 r41210) * checking for file 'prism/DESCRIPTION' ... OK * this is package 'prism' version '0.1.1' * 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 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 ... 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 ... 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 '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 for CRLF line endings in C/C++/Fortran sources/headers ... 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 /loc/biocbuild/bbs-2.1-bioc/meat/prism.Rcheck/00check.log for details
prism.Rcheck/00install.out:
* Installing *source* package 'prism' ... ** libs gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -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: 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: 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_mcmc': bisegment.c:1285: warning: control reaches end of non-void function bisegment.c: In function 'bisegment': bisegment.c:460: warning: control reaches end of non-void function gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -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 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -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 gcc -std=gnu99 -G -L/usr/local/lib -o prism.so bisegment.o find_grid.o util.o -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading Loading required package: EBImage Creating a new generic function for "summary" in "prism" ** help >>> Building/Updating help pages for package 'prism' Formats: text html latex example extractExpression text html latex example formImagePair text html latex example getGrid text html latex example like text html latex plotEstimates text html latex example prism text html latex example prismEstimates-class text html latex example prismGrid-class text html latex example prismImage-class text html latex example ** building package indices ... * DONE (prism)