CHECK report for prism on churchill

* checking for working latex ... OK * using log directory '/loc/biocbuild/2.0d/Rpacks/prism.Rcheck' * using R version 2.5.0 Under development (unstable) (2006-12-05 r40126) * checking for file 'prism/DESCRIPTION' ... OK * this is package 'prism' version '0.1.1' * checking package dependencies ... WARNING 'library' or 'require' calls not declared from: methods 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 ... WARNING Loading required package: EBImage Loading required package: methods Error in paste("... EBImage", packageDescription("EBImage", fields = "Version"), : could not find function "packageDescription" Error: .onLoad failed in 'loadNamespace' for 'EBImage' Error: package 'EBImage' could not be loaded Execution halted It looks like this package (or one of its dependent packages) has an unstated dependence on a standard package. All dependencies must be declared in DESCRIPTION. See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. * checking whether the name space can be loaded with stated dependencies ... WARNING Loading required package: methods Error in paste("... EBImage", packageDescription("EBImage", fields = "Version"), : could not find function "packageDescription" Error: .onLoad failed in 'loadNamespace' for 'EBImage' Error: unable to load R code in package 'prism' Execution halted A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 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 4 warnings, see /loc/biocbuild/2.0d/Rpacks/prism.Rcheck/00check.log for details

* Installing *source* package 'prism' ... ** 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 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/2.0d/R/include -I/loc/biocbuild/2.0d/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/2.0d/R/include -I/loc/biocbuild/2.0d/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 ** R ** data ** inst ** save image Loading required package: EBImage ... EBImage 1.5.007 ... ** 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 152/208	OS	Arch	BUILD	CHECK	BUILD BIN
prism 0.1.1 Raphael Gottardo	Linux (SUSE 9.2)	x86_64	ERROR	skipped
	Linux (SUSE 10.1)	x86_64	ERROR	skipped
	Linux (SUSE 9.2)	i686	ERROR	skipped
	Solaris 2.9	sparc	OK	[ WARNINGS ]
	Windows Server 2003	x86_64	ERROR	skipped	skipped
	Windows Server 2003	NA	ERROR	skipped	skipped
	Mac OS X (10.4.6)	i686	ERROR	skipped

prism

0.1.1

Command output