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Package 56/671HostnameOS / ArchBUILDCHECKBUILD BIN
BayesPeak 1.12.0
Jonathan Cairns
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/BayesPeak
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: BayesPeak
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BayesPeak_1.12.0.tar.gz
StartedAt: 2013-05-01 02:37:02 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 02:47:21 -0700 (Wed, 01 May 2013)
EllapsedTime: 619.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BayesPeak.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BayesPeak.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 'BayesPeak/DESCRIPTION' ... OK
* this is package 'BayesPeak' version '1.12.0'
* 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 'BayesPeak' can be installed ... [10s/12s] OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   5.0Mb
* 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 ... NOTE
S3 methods shown with full name in documentation object 'overfittingDiagnostics':
  'plot.overfitdiag' 'identify.overfitdiag'

S3 methods shown with full name in documentation object 'plot.PP':
  'plot.PP'

S3 methods shown with full name in documentation object 'plot.bed':
  'plot.bed'

S3 methods shown with full name in documentation object 'plot.job':
  'plot.job'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/BayesPeak.Rcheck/BayesPeak/libs/BayesPeak.so':
  Found '___stdoutp', possibly from 'stdout' (C)
    Object: 'bayespeak.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [499s/521s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bayespeak       241.809  1.056 249.011
summarise.peaks 235.492  1.297 251.625
plot.job         10.342  0.214  10.995
* 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

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/BayesPeak.Rcheck/00check.log'
for details.

BayesPeak.Rcheck/00install.out:

* installing *source* package 'BayesPeak' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c bayespeak.c -o bayespeak.o
In file included from bayespeak.c:9:
./bayespeak_gsl.h:40:22: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
      long int h = s / q1;
               ˜   ˜˜^˜˜˜
./bayespeak_gsl.h:41:38: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
      long int t = a1 * (s - h * q1) - h * r1;
               ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./bayespeak_gsl.h:41:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
      long int t = a1 * (s - h * q1) - h * r1;
                           ˜ ˜˜^˜˜˜
./bayespeak_gsl.h:41:42: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
      long int t = a1 * (s - h * q1) - h * r1;
                                     ˜ ˜˜^˜˜˜
./bayespeak_gsl.h:44:11: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
      s = t;
        ˜ ^
./bayespeak_gsl.h:49:22: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
      long int h = s / q1;
               ˜   ˜˜^˜˜˜
./bayespeak_gsl.h:50:38: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
      long int t = a1 * (s - h * q1) - h * r1;
               ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./bayespeak_gsl.h:50:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
      long int t = a1 * (s - h * q1) - h * r1;
                           ˜ ˜˜^˜˜˜
./bayespeak_gsl.h:50:42: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
      long int t = a1 * (s - h * q1) - h * r1;
                                     ˜ ˜˜^˜˜˜
./bayespeak_gsl.h:53:11: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
      s = t;
        ˜ ^
./bayespeak_gsl.h:74:19: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
  long int h1 = x / q1;
           ˜˜   ˜˜^˜˜˜
./bayespeak_gsl.h:75:36: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
  long int t1 = a1 * (x - h1 * q1) - h1 * r1;
           ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./bayespeak_gsl.h:75:30: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
  long int t1 = a1 * (x - h1 * q1) - h1 * r1;
                        ˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:75:41: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
  long int t1 = a1 * (x - h1 * q1) - h1 * r1;
                                   ˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:77:19: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
  long int h2 = y / q2;
           ˜˜   ˜˜^˜˜˜
./bayespeak_gsl.h:78:36: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
  long int t2 = a2 * (y - h2 * q2) - h2 * r2;
           ˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./bayespeak_gsl.h:78:30: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
  long int t2 = a2 * (y - h2 * q2) - h2 * r2;
                        ˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:78:41: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
  long int t2 = a2 * (y - h2 * q2) - h2 * r2;
                                   ˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:86:14: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
  state->x = t1;
           ˜ ^˜
./bayespeak_gsl.h:87:14: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
  state->y = t2;
           ˜ ^˜
./bayespeak_gsl.h:91:40: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
    long int delta = state->shuffle[j] - t2;
             ˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./bayespeak_gsl.h:91:42: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    long int delta = state->shuffle[j] - t2;
                                       ˜ ^˜
./bayespeak_gsl.h:94:16: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    state->n = delta;
             ˜ ^˜˜˜˜
./bayespeak_gsl.h:95:25: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    state->shuffle[j] = t1;
                      ˜ ^˜
bayespeak.c:38:12: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
        return (1 - gsl_cdf_ugaussian_Q (x));
        ˜˜˜˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bayespeak.c:43:9: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
        return logfact(n);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
bayespeak.c:155:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        stateZ = (int*) R_alloc(N, sizeof(int));
                        ˜˜˜˜˜˜˜ ^
bayespeak.c:156:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        scorepos = (double*) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
bayespeak.c:157:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        scoreneg = (double*) R_alloc(N, sizeof(double));
                             ˜˜˜˜˜˜˜ ^
bayespeak.c:158:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        probX = (double*) R_alloc(N, sizeof(double));
                          ˜˜˜˜˜˜˜ ^
bayespeak.c:173:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int burnin = ceil(iters/2); //, na = ceil(iters*11/20), nstar = ceil(iters*3/4);
      ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
bayespeak.c:238:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *gamma_pow = (double*) R_alloc((*w_max + 2), sizeof(double));
                                      ˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜^˜˜
bayespeak.c:248:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *gammanew_pow = (double*) R_alloc((*w_max + 2), sizeof(double));
                                         ˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜^˜˜
bayespeak.c:256:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  probZ = (double**) R_alloc(N, sizeof(double*));
                     ˜˜˜˜˜˜˜ ^
bayespeak.c:267:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                Y[i] = (double*) R_alloc(N, sizeof(double));
                                 ˜˜˜˜˜˜˜ ^
bayespeak.c:268:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                cdfZ[i] = (double*) R_alloc(N, sizeof(double));
                                    ˜˜˜˜˜˜˜ ^
bayespeak.c:269:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                P2[i] = (double*) R_alloc(N, sizeof(double));
                                  ˜˜˜˜˜˜˜ ^
bayespeak.c:540:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                                c0 = normald(-a0/sd0); 
                                     ˜˜˜˜˜˜˜ ˜˜˜^˜˜˜
bayespeak.c:541:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                                c1 = normald(-a1/sd1);
                                     ˜˜˜˜˜˜˜ ˜˜˜^˜˜˜
bayespeak.c:542:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                                c2 = normald(-gamma/sd2);
                                     ˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜
bayespeak.c:543:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                                cc0 = normald(-aa0/sd0); 
                                      ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜
bayespeak.c:544:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                                cc1 = normald(-aa1/sd1);
                                      ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜
bayespeak.c:545:28: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                                cc2 = normald(-gammanew/sd2);
                                      ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜
43 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 BayesPeak.so bayespeak.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BayesPeak.Rcheck/BayesPeak/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 (BayesPeak)

BayesPeak.Rcheck/BayesPeak-Ex.timings:

nameusersystemelapsed
bayespeak241.809 1.056249.011
overfitting0.2020.0230.235
plot.PP0.1600.0140.187
plot.bed2.1170.0622.216
plot.job10.342 0.21410.995
read.bed1.8850.0491.984
summarise.peaks235.492 1.297251.625