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Package 656/671HostnameOS / ArchBUILDCHECKBUILD BIN
Vega 1.8.0
Sandro Morganella
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Vega
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: Vega
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Vega_1.8.0.tar.gz
StartedAt: 2013-05-01 11:39:03 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:39:28 -0700 (Wed, 01 May 2013)
EllapsedTime: 25.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Vega.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Vega.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Vega/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Vega' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Vega' can be installed ... [2s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

Vega.Rcheck/00install.out:

* installing *source* package 'Vega' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c vega.c -o vega.o
vega.c:251:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a->elements = (node_ptr)malloc(sizeof(node)*((a->max_elems)+1));
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
vega.c:369:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        lambda_gradient = abs(lambda);
                          ˜˜˜ ^˜˜˜˜˜
vega.c:390:48: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                tmp_lambda = update_priority(brks, brk_del.prev);
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜˜˜˜^˜˜˜
vega.c:405:48: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                tmp_lambda = update_priority(brks, brk_del.next);
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜˜˜˜^˜˜˜
vega.c:447:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                i=brk_del.next;
                 ˜˜˜˜˜˜˜˜˜^˜˜˜
vega.c:348:68: warning: unused variable 'tmp_lambda2' [-Wunused-variable]
        double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
                                                                          ^
vega.c:355:13: warning: unused variable 'maxptr' [-Wunused-variable]
        node max, *maxptr, tmp_node;
                   ^
vega.c:347:6: warning: unused variable 'index' [-Wunused-variable]
        int index;
            ^
vega.c:470:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                heap_insert(&s, node_create(i, (float) -(brks[i].size)));
                                ˜˜˜˜˜˜˜˜˜˜˜ ^
vega.c:471:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                i=brks[i].next;
                 ˜˜˜˜˜˜˜˜˜^˜˜˜
vega.c:490:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                tmp_lambda = update_priority(brks, curr.id);
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜^˜
vega.c:493:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                        tmp_lambda = update_priority(brks, next.next);
                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜^˜˜˜
vega.c:496:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                brks[next.id].prev = -2;
                                                   ˜ ^˜
vega.c:504:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        brks[0].next = num_of_probes;
                                                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
vega.c:508:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        curr.prev = -2;
                                                  ˜ ^˜
vega.c:513:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                brks[prev.id].next = num_of_probes;
                                                                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
vega.c:517:47: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                                tmp_lambda = update_priority(brks, prev.id);
                                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜^˜
vega.c:529:48: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                                        tmp_lambda = update_priority(brks, prev.id);
                                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜^˜
vega.c:531:48: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                                        tmp_lambda = update_priority(brks, next.id);
                                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜^˜
vega.c:539:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                        brks[next.id].prev = -2;
                                                                           ˜ ^˜
vega.c:540:48: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                                        tmp_lambda = update_priority(brks, curr.id);
                                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜^˜
vega.c:546:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                                                tmp_lambda = update_priority(brks, next.next);
                                                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜^˜˜˜
vega.c:564:20: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        prev_id = brks[i].prev; 
                ˜ ˜˜˜˜˜˜˜˜^˜˜˜
vega.c:560:64: warning: unused variable 'next_mean' [-Wunused-variable]
        double lambda, first_term, second_term, prev_mean, curr_mean, next_mean;
                                                                      ^
vega.c:588:78: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        brks[0] = breakpoint_create(0, -1, floor(*(data)*ROUND_CNST)/ROUND_CNST, 1, -1, 1);
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                 ^˜
vega.c:591:42: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        brks[num_of_probes] = breakpoint_create(num_of_probes, -1, -1, -1, -1, -1);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
vega.c:591:69: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        brks[num_of_probes] = breakpoint_create(num_of_probes, -1, -1, -1, -1, -1);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                            ^˜
vega.c:591:73: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        brks[num_of_probes] = breakpoint_create(num_of_probes, -1, -1, -1, -1, -1);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                ^˜
vega.c:604:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                brks[i] = breakpoint_create(i, -tmp_lambda, floor(*(data+(i))*ROUND_CNST)/ROUND_CNST, 1, i-1, i+1);
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
vega.c:604:93: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                brks[i] = breakpoint_create(i, -tmp_lambda, floor(*(data+(i))*ROUND_CNST)/ROUND_CNST, 1, i-1, i+1);
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                              ˜^˜
vega.c:604:98: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                brks[i] = breakpoint_create(i, -tmp_lambda, floor(*(data+(i))*ROUND_CNST)/ROUND_CNST, 1, i-1, i+1);
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                                   ˜^˜
vega.c:606:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                heap_insert(b,node_create(i, -tmp_lambda));
                              ˜˜˜˜˜˜˜˜˜˜˜ ^
32 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Vega.so vega.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Vega.Rcheck/Vega/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Vega)

Vega.Rcheck/Vega-Ex.timings:

nameusersystemelapsed
Vega-package0.6760.0270.712
plotSegmentation1.3990.0591.525
vega0.5720.0160.652