Package: prism

Version: 0.1.1

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build prism

RetCode: 0

Time: 33.4 seconds

Status: OK

PackageFile: prism_0.1.1.tar.gz

* checking for file 'prism/DESCRIPTION' ... OK
* preparing 'prism':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* 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
** save image
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)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'prism_0.1.1.tar.gz'