CHECK report for prism on gopher5

* checking for working latex ... OK * using log directory '/loc/biocbuild/1.9d/Rpacks/prism.Rcheck' * using R version 2.4.0 alpha (2006-09-10 r39242) * checking for file 'prism/DESCRIPTION' ... OK * this is package 'prism' version '0.1.1' * checking package dependencies ... WARNING package 'methods' is used but not declared 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 '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 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 whether the name space 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 ... OK * 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 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 was 1 warning, see /loc/biocbuild/1.9d/Rpacks/prism.Rcheck/00check.log for details

* Installing *source* package 'prism' ... ** libs gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -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: 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: 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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -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:856: warning: `J' might be used uninitialized in this function util.c:856: warning: `K' might be used uninitialized in this function gcc -shared -L/usr/local/lib64 -o prism.so bisegment.o find_grid.o util.o ** R ** data ** inst ** save image Loading required package: EBImage .: EBImage of Bioconductor.org :. ** 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)

Package 149/205	OS	Arch	BUILD	CHECK	BUILD BIN
prism 0.1.1 Raphael Gottardo	Linux (SUSE 9.2)	x86_64	OK	[ WARNINGS ]
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	OK	OK
	Linux (SUSE 10.0)	x86_64	OK	WARNINGS
	Windows Server 2003	x86_64	ERROR	skipped	skipped
	Windows XP	i686	ERROR	skipped	skipped
	Mac OS X (10.4.6)	i686	ERROR	skipped

prism

0.1.1

Command output