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Package 316/671HostnameOS / ArchBUILDCHECKBUILD BIN
HMMcopy 1.2.0
Daniel Lai , Gavin Ha , Sohrab Shah
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/HMMcopy
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: HMMcopy
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HMMcopy_1.2.0.tar.gz
StartedAt: 2013-05-01 06:50:58 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 06:53:45 -0700 (Wed, 01 May 2013)
EllapsedTime: 167.0 seconds
RetCode: 0
Status:  OK 
CheckDir: HMMcopy.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HMMcopy.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 'HMMcopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HMMcopy' version '1.2.0'
* 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 'HMMcopy' can be installed ... [15s/15s] 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 ... [23s/24s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
HMMcopy-package 10.711  0.843   11.86
* 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

HMMcopy.Rcheck/00install.out:

* installing *source* package 'HMMcopy' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c forward_backward.c -o forward_backward.o
forward_backward.c:35:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  transposeSquareInPlace(transmatT, transmat, K);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                      ^
forward_backward.c:63:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  multiplyInPlace(alpha + t * K, init_state_distrib, obslik + t * K, K);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                    ^
forward_backward.c:64:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  scale[t] = normalizeInPlace(alpha + t * K, K);
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                ^
forward_backward.c:72:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    multiplyMatrixInPlace(m, transmatT, alpha + (t - 1) * K, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                    ^
forward_backward.c:73:55: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    multiplyInPlace(alpha + t * K, m, obslik + t * K, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                   ^
forward_backward.c:74:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    scale[t] = normalizeInPlace(alpha + t * K, K);
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                ^
forward_backward.c:112:66: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    multiplyInPlace(b, beta + (t + 1) * K, obslik + (t + 1) * K, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                              ^
forward_backward.c:113:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    multiplyMatrixInPlace(m, transmat, b, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^
forward_backward.c:114:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    normalizeInPlace(m, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^
forward_backward.c:121:58: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    outerProductUVInPlace(squareSpace, alpha + t * K, b, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                ^
forward_backward.c:123:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      eta + t * K * K, transmat, squareSpace, K * K);
                                              ˜˜^˜˜
forward_backward.c:124:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    normalizeInPlace(eta + t * K * K, K * K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                  ˜˜^˜˜
forward_backward.c:127:53: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    multiplyInPlace(m, alpha + t * K, beta + t * K, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                 ^
forward_backward.c:128:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    normalizeInPlace(m, K);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜    ^
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c register.c -o register.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c viterbi.c -o viterbi.o
viterbi.c:50:52: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  addVectors(delta + t * K, prior, obslik + t * K, K);
  ˜˜˜˜˜˜˜˜˜˜                                       ^
viterbi.c:51:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  setVectorToValue_int(psi + t * K, 0, K);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^
viterbi.c:56:60: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      addVectors(d, delta + (t - 1) * K, transmat + j * K, K);
      ˜˜˜˜˜˜˜˜˜˜                                           ^
viterbi.c:57:63: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      maxVectorInPlace(delta + j + t * K, psi + j + t * K, d, K);
      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                        ^
viterbi.c:64:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  maxVectorInPlace(d, path + t, delta + t * K, K); // Use d[0] as temp variable
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                             ^
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
viterbi.c:144:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      index = i;
            ˜ ^
7 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 HMMcopy.so forward_backward.o register.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/HMMcopy.Rcheck/HMMcopy/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 (HMMcopy)

HMMcopy.Rcheck/HMMcopy-Ex.timings:

nameusersystemelapsed
HMMcopy-input0.2300.0140.245
HMMcopy-output0.3320.0650.414
HMMcopy-package10.711 0.84311.860
HMMcopy-visualize1.2140.0961.404
HMMsegment0.5240.0760.605
correctReadcount0.9250.0220.956
wigsToRangedData0.2980.0380.344