RchyOptimyx 1.4.0
Adrin Jalali , Nima Aghaeepour
| 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/RchyOptimyx | | 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 |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RchyOptimyx.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 'RchyOptimyx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RchyOptimyx' 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 'RchyOptimyx' can be installed ... [7s/9s] 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 ... [10s/10s] 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
* installing *source* package 'RchyOptimyx' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c RchyOptimyx.cpp -o RchyOptimyx.o
In file included from RchyOptimyx.cpp:13:
./graehl/graph.h:75:8: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
pred = pred; // dummy statement to avoid warnings
˜˜˜˜ ^ ˜˜˜˜
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:279:
./graehl/kbest.h:37:9: warning: explicitly assigning a variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
dummy = dummy;
˜˜˜˜˜ ^ ˜˜˜˜˜
./graehl/kbest.h:44:42: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
freeList = (GraphHeap *)::operator new(newBlocksize * sizeof(GraphHeap));
^˜˜˜˜˜˜˜˜˜˜˜ ˜
RchyOptimyx.cpp:69:16: warning: implicit conversion changes signedness: 'mapped_type' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (!visited[graphIdMap[neighbor.text()]])
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RchyOptimyx.cpp:75:10: warning: implicit conversion changes signedness: 'mapped_type' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
visited[graphIdMap[n.text()]] = true;
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RchyOptimyx.cpp:81:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
g.nStates = pow(2.0, dest.nonZeroCount());
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RchyOptimyx.cpp:139:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return i;
˜˜˜˜˜˜ ^
RchyOptimyx.cpp:236:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tmp = '0' + s_values[i * protein_count + j];
˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RchyOptimyx.cpp:312:79: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned char' [-Wconversion]
unsigned char scaled_value = (unsigned char)255 * (it->second - min_score) / (max_score - min_score);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RchyOptimyx.cpp:332:30: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float scaled_value = jt->second;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
RchyOptimyx.cpp:342:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (jt->first[diff_pos] == '1')
˜˜ ^˜˜˜˜˜˜˜
RchyOptimyx.cpp:247:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
NumberGenerator dest(strlen(back_trace_start), 3, back_trace_start);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RchyOptimyx.cpp:250:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
NumberGenerator source(strlen(back_trace_start), 3, start.c_str());
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RchyOptimyx.cpp:359:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char **matrix = (char **)calloc(x, sizeof(char*));
˜˜˜˜˜˜ ^
RchyOptimyx.cpp:362:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matrix[i] = (char *)calloc(y, sizeof(char));
˜˜˜˜˜˜ ^
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:6:
./graehl/2heap.h:48:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int heapSize = heapEnd - heapStart;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
./graehl/graph.h:173:5: note: in instantiation of function template specialization 'heapPop<DistToState>' requested here
heapPop(distQueue, distQueue + nUnknown--);
^
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:6:
./graehl/2heap.h:70:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int parent, current = element - heap;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜
./graehl/graph.h:182:2: note: in instantiation of function template specialization 'heapAdjustUp<DistToState>' requested here
heapAdjustUp(distQueue, stateLocations[targetState]);
^
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:6:
./graehl/2heap.h:16:19: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int i = heapEnd - heap;
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜
./graehl/kbest.h:153:5: note: in instantiation of function template specialization 'heapAdd<EdgePath>' requested here
heapAdd(pathQueue, endQueue++, newPath);
^
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:6:
./graehl/2heap.h:8:12: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
return e - s;
˜˜˜˜˜˜ ˜˜^˜˜
./graehl/kbest.h:154:13: note: in instantiation of function template specialization 'heapSize<EdgePath>' requested here
while ( heapSize(pathQueue, endQueue) && --k ) {
^
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:6:
./graehl/2heap.h:48:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int heapSize = heapEnd - heapStart;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
./graehl/kbest.h:188:6: note: in instantiation of function template specialization 'heapPop<EdgePath>' requested here
heapPop(pathQueue, endQueue--);
^
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:6:
./graehl/2heap.h:85:22: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int size = heapEnd - heapStart;
˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
./graehl/kbest.h:321:4: note: in instantiation of function template specialization 'heapBuild<pGraphArc>' requested here
heapBuild(heapStart, heapStart + heapSize);
^
21 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c dataRead.cpp -o dataRead.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mystring.cpp -o mystring.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c numberGenerator.cpp -o numberGenerator.o
numberGenerator.cpp:34:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(this->_data, other._data, len);
˜˜˜˜˜˜ ^˜˜
numberGenerator.cpp:35:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(this->_text, other._text, len + 1);
˜˜˜˜˜˜ ˜˜˜˜^˜˜
numberGenerator.cpp:46:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(this->_data, other._data, len);
˜˜˜˜˜˜ ^˜˜
numberGenerator.cpp:47:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(this->_text, other._text, len + 1);
˜˜˜˜˜˜ ˜˜˜˜^˜˜
numberGenerator.cpp:70:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memset(_data, 0, len);
˜˜˜˜˜˜ ^˜˜
numberGenerator.cpp:175:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(result._data, _data, len);
˜˜˜˜˜˜ ^˜˜
6 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 RchyOptimyx.so RchyOptimyx.o dataRead.o mystring.o numberGenerator.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/RchyOptimyx.Rcheck/RchyOptimyx/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'RchyOptimyx'
Creating a new generic function for 'merge' in package 'RchyOptimyx'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RchyOptimyx)