Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 52/671HostnameOS / ArchBUILDCHECKBUILD BIN
ASEB 1.4.0
Likun Wang
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/ASEB
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: ASEB
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ASEB_1.4.0.tar.gz
StartedAt: 2013-05-01 02:32:47 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 02:33:51 -0700 (Wed, 01 May 2013)
EllapsedTime: 63.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ASEB.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ASEB.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 'ASEB/DESCRIPTION' ... OK
* this is package 'ASEB' version '1.4.0'
* 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 'ASEB' can be installed ... [4s/4s] 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 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 ... [34s/35s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
drawStat     8.437  0.050   8.605
asebProteins 8.202  0.085   8.380
drawEScurve  6.060  0.065   6.231
asebSites    5.764  0.064   5.916
* 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

ASEB.Rcheck/00install.out:

* installing *source* package 'ASEB' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c asebC.cpp -o asebC.o
asebC.cpp:295:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if(sequence[i] == 'K'){
                   ˜˜˜˜˜˜˜˜ ^
asebC.cpp:296:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                   string site_seq = sequence.substr(i-8, 17);
                                     ˜˜˜˜˜˜˜˜        ˜^˜
asebC.cpp:311:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
         if(sequence[i] == 'K'){
            ˜˜˜˜˜˜˜˜ ^
asebC.cpp:312:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            string site_seq = sequence.substr(i-8, 17);
                              ˜˜˜˜˜˜˜˜        ˜^˜
asebC.cpp:329:78: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       int score = get_score_seqs(id2seq[protein_name], id2seq[total_poteins[i]]);
                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:330:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       score_matrix.push_back(pair<string, int>(total_poteins[i], score));
                                                ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:346:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       if(score_matrix[i].second > 0){
          ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:347:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          score_matrix[i].second = score_matrix[i].second/max_pos;
          ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:347:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          score_matrix[i].second = score_matrix[i].second/max_pos;
                                   ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:349:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       if(score_matrix[i].second < 0){
          ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:350:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          score_matrix[i].second = score_matrix[i].second/min_neg;
          ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:350:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          score_matrix[i].second = score_matrix[i].second/min_neg;
                                   ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:352:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       geneName2rank[score_matrix[i].first] = i;
                     ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:368:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
   indexes.reserve(size);
   ˜˜˜˜˜˜˜         ^˜˜˜
asebC.cpp:365:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   int max = score_matrix.size();
       ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:366:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   int size = predefined.size();
       ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:400:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      random_index.push_back(geneName2rank[total_poteins[rand_num2]]);
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
asebC.cpp:390:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   int max = total_poteins.size();
       ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:424:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       rand_str[i] = str1[indexes[i]];
       ˜˜˜˜˜˜˜˜ ^
asebC.cpp:424:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       rand_str[i] = str1[indexes[i]];
                     ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:424:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       rand_str[i] = str1[indexes[i]];
                          ˜˜˜˜˜˜˜ ^
asebC.cpp:428:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       rand_str[i] = str1[indexes[i-1]];
       ˜˜˜˜˜˜˜˜ ^
asebC.cpp:428:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       rand_str[i] = str1[indexes[i-1]];
                     ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:428:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
       rand_str[i] = str1[indexes[i-1]];
                          ˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:414:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   int size = str1.size();
       ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
asebC.cpp:540:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char chr1 = str1[i];
                    ˜˜˜˜ ^
asebC.cpp:541:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char chr2 = str2[i];
                    ˜˜˜˜ ^
asebC.cpp:569:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if(score_matrix[indexes[i]].second > 0){
           ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:569:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if(score_matrix[indexes[i]].second > 0){
                        ˜˜˜˜˜˜˜ ^
asebC.cpp:570:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr+=score_matrix[indexes[i]].second;
               ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:570:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr+=score_matrix[indexes[i]].second;
                            ˜˜˜˜˜˜˜ ^
asebC.cpp:572:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr-=score_matrix[indexes[i]].second;
               ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:572:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr-=score_matrix[indexes[i]].second;
                            ˜˜˜˜˜˜˜ ^
asebC.cpp:575:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ES_current = (score_matrix[indexes[0]].second/Nr)-(double)indexes[0]/(N-Nh);
                  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:581:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                       ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:581:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                                    ˜˜˜˜˜˜˜ ^
asebC.cpp:581:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                                                                    ˜˜˜˜˜˜˜ ^
asebC.cpp:581:89: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                                                                               ˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:565:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int N = score_matrix.size();
        ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:597:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if(score_matrix[indexes[i]].second > 0){
           ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:597:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if(score_matrix[indexes[i]].second > 0){
                        ˜˜˜˜˜˜˜ ^
asebC.cpp:598:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr+=score_matrix[indexes[i]].second;
               ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:598:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr+=score_matrix[indexes[i]].second;
                            ˜˜˜˜˜˜˜ ^
asebC.cpp:600:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr-=score_matrix[indexes[i]].second;
               ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:600:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
           Nr-=score_matrix[indexes[i]].second;
                            ˜˜˜˜˜˜˜ ^
asebC.cpp:605:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ES_current = (score_matrix[indexes[0]].second/Nr)-(double)indexes[0]/(N-Nh);
                  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:607:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    line2 += double2str(ES_current-score_matrix[indexes[0]].second/Nr)+"\t";
                                   ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:615:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                       ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:615:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                                    ˜˜˜˜˜˜˜ ^
asebC.cpp:615:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                                                                    ˜˜˜˜˜˜˜ ^
asebC.cpp:615:89: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ES_current += (score_matrix[indexes[i]].second/Nr)-(double)(indexes[i]-indexes[i-1]-1)/(N-Nh);
                                                                               ˜˜˜˜˜˜˜ ˜^˜
asebC.cpp:620:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        line1 += int2str(indexes[i])+"\t";
                         ˜˜˜˜˜˜˜ ^
asebC.cpp:621:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        line2 += double2str(ES_current-score_matrix[indexes[i]].second/Nr)+"\t";
                                       ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
asebC.cpp:621:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        line2 += double2str(ES_current-score_matrix[indexes[i]].second/Nr)+"\t";
                                                    ˜˜˜˜˜˜˜ ^
asebC.cpp:622:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        line1 += int2str(indexes[i]+1)+"\t";
                         ˜˜˜˜˜˜˜ ^
asebC.cpp:593:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int N = score_matrix.size();
        ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:625:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    line1 += int2str(score_matrix.size())+"\t";
             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
asebC.cpp:634:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if(predefined.count(score_matrix[i].first) != 0){
                            ˜˜˜˜˜˜˜˜˜˜˜˜ ^
asebC.cpp:644:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if(predefined.count(score_matrix[i].first) != 0){
                            ˜˜˜˜˜˜˜˜˜˜˜˜ ^
59 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 ASEB.so asebC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ASEB.Rcheck/ASEB/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ASEB)

ASEB.Rcheck/ASEB-Ex.timings:

nameusersystemelapsed
SequenceInfo0.0090.0020.011
asebProteins8.2020.0858.380
asebSites5.7640.0645.916
drawEScurve6.0600.0656.231
drawStat8.4370.0508.605
readSequence4.3990.0504.490