ChemmineR 2.12.2
ChemmineR Team
| 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/ChemmineR | | Last Changed Rev: 76049 / Revision: 76155 | | Last Changed Date: 2013-04-25 19:32:34 -0700 (Thu, 25 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/ChemmineR.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 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '2.12.2'
* 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 'ChemmineR' can be installed ... [12s/13s] 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 ... NOTE
Found the following possibly unsafe calls:
File 'ChemmineR/R/sim.R':
unlockBinding(".progress_bar_int_cnt", environment(.progress_bar))
.data.frame.to.str: no visible binding for global variable 'string'
* checking Rd files ... NOTE
prepare_Rd: batchByIndex.Rd:27-29: Dropping empty section \details
prepare_Rd: batchByIndex.Rd:30-36: Dropping empty section \value
prepare_Rd: batchByIndex.Rd:43-45: Dropping empty section \note
prepare_Rd: batchByIndex.Rd:40-42: Dropping empty section \author
prepare_Rd: batchByIndex.Rd:37-39: Dropping empty section \references
prepare_Rd: batchByIndex.Rd:49-51: Dropping empty section \seealso
prepare_Rd: bufferLines.Rd:25-27: Dropping empty section \details
prepare_Rd: bufferLines.Rd:28-34: Dropping empty section \value
prepare_Rd: bufferLines.Rd:41-43: Dropping empty section \note
prepare_Rd: bufferLines.Rd:38-40: Dropping empty section \author
prepare_Rd: bufferLines.Rd:35-37: Dropping empty section \references
prepare_Rd: bufferLines.Rd:47-49: Dropping empty section \seealso
prepare_Rd: bufferResultSet.Rd:28-30: Dropping empty section \details
prepare_Rd: bufferResultSet.Rd:31-37: Dropping empty section \value
prepare_Rd: bufferResultSet.Rd:44-46: Dropping empty section \note
prepare_Rd: bufferResultSet.Rd:41-43: Dropping empty section \author
prepare_Rd: bufferResultSet.Rd:38-40: Dropping empty section \references
prepare_Rd: bufferResultSet.Rd:50-52: Dropping empty section \seealso
prepare_Rd: jarvisPatrick_c.Rd:40-42: Dropping empty section \details
prepare_Rd: jarvisPatrick_c.Rd:43-49: Dropping empty section \value
prepare_Rd: jarvisPatrick_c.Rd:56-58: Dropping empty section \note
prepare_Rd: jarvisPatrick_c.Rd:53-55: Dropping empty section \author
prepare_Rd: jarvisPatrick_c.Rd:50-52: Dropping empty section \references
prepare_Rd: jarvisPatrick_c.Rd:62-64: Dropping empty section \seealso
prepare_Rd: jarvisPatrick_c.Rd:65-67: Dropping empty section \examples
prepare_Rd: selectInBatches.Rd:30-32: Dropping empty section \details
prepare_Rd: selectInBatches.Rd:33-39: Dropping empty section \value
prepare_Rd: selectInBatches.Rd:46-48: Dropping empty section \note
prepare_Rd: selectInBatches.Rd:43-45: Dropping empty section \author
prepare_Rd: selectInBatches.Rd:40-42: Dropping empty section \references
prepare_Rd: selectInBatches.Rd:52-54: Dropping empty section \seealso
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs/ChemmineR.so':
Found '__ZSt4cerr', possibly from 'std::cerr' (C++)
Objects: 'desc.o', 'formats.o', 'script.o'
Found '__ZSt4cout', possibly from 'std::cout' (C++)
Object: 'cluster.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 ... [77s/78s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
jarvisPatrick 7.434 0.489 8.055
trimNeighbors 5.570 0.066 5.742
addNewFeatures 5.083 0.209 5.456
loadSdf 5.104 0.091 5.255
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'runTests.R' [29s/29s]
[29s/30s] 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
NOTE: There were 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.
* installing *source* package 'ChemmineR' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c DisjointSets.cpp -o DisjointSets.o
DisjointSets.cpp:31:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes.resize(m_numElements);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
DisjointSets.cpp:33:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i] = new Node(*s.m_nodes[i]);
˜˜˜˜˜˜˜ ^
DisjointSets.cpp:33:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i] = new Node(*s.m_nodes[i]);
˜ ^
DisjointSets.cpp:37:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(m_nodes[i]->parent != NULL)
˜˜˜˜˜˜˜ ^
DisjointSets.cpp:38:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i]->parent = m_nodes[s.m_nodes[i]->parent->index];
˜˜˜˜˜˜˜ ^
DisjointSets.cpp:38:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i]->parent = m_nodes[s.m_nodes[i]->parent->index];
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
DisjointSets.cpp:38:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i]->parent = m_nodes[s.m_nodes[i]->parent->index];
˜ ^
DisjointSets.cpp:44:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
delete m_nodes[i];
˜˜˜˜˜˜˜ ^
DisjointSets.cpp:58:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
curNode = m_nodes[elementId];
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
DisjointSets.cpp:65:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
curNode = m_nodes[elementId];
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
DisjointSets.cpp:82:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Node* set1 = m_nodes[setId1];
˜˜˜˜˜˜˜ ^˜˜˜˜˜
DisjointSets.cpp:83:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Node* set2 = m_nodes[setId2];
˜˜˜˜˜˜˜ ^˜˜˜˜˜
DisjointSets.cpp:108:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes.insert(m_nodes.end(), numToAdd, (Node*)NULL);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
DisjointSets.cpp:111:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i] = new Node();
˜˜˜˜˜˜˜ ^
DisjointSets.cpp:112:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i]->parent = NULL;
˜˜˜˜˜˜˜ ^
DisjointSets.cpp:113:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i]->index = i;
˜˜˜˜˜˜˜ ^
DisjointSets.cpp:114:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_nodes[i]->rank = 0;
˜˜˜˜˜˜˜ ^
17 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cluster.cc -o cluster.o
In file included from cluster.cc:9:
./debug.h:9:25: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define DEBUG_PRINT(fmt,...)
^
cluster.cc:104:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int to_erase = nbrs.size() - p;
˜ ^
cluster.cc:104:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int to_erase = nbrs.size() - p;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
cluster.cc:119:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (nbrs1[i] == nbrs2[j]) {
˜˜˜˜˜ ^
cluster.cc:119:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (nbrs1[i] == nbrs2[j]) {
˜˜˜˜˜ ^
cluster.cc:122:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
} else if (nbrs1[i] > nbrs2[j])
˜˜˜˜˜ ^
cluster.cc:122:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
} else if (nbrs1[i] > nbrs2[j])
˜˜˜˜˜ ^
cluster.cc:132:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(x==list[i])
˜˜˜˜ ^
cluster.cc:165:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (nbr_intersect(nbr_list[i], nbr_list[j]) < m)
˜˜˜˜˜˜˜˜ ^
cluster.cc:165:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (nbr_intersect(nbr_list[i], nbr_list[j]) < m)
˜˜˜˜˜˜˜˜ ^
cluster.cc:172:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int minPairsNeeded = (cluster_members[si].size() * cluster_members[sj].size() + 1 ) / 2;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:172:71: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int minPairsNeeded = (cluster_members[si].size() * cluster_members[sj].size() + 1 ) / 2;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:177:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator k = cluster_members[si].begin(); k != cluster_members[si].end(); k++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:177:82: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator k = cluster_members[si].begin(); k != cluster_members[si].end(); k++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:179:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator l = cluster_members[sj].begin(); l != cluster_members[sj].end(); l++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:179:83: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator l = cluster_members[sj].begin(); l != cluster_members[sj].end(); l++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:182:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(nbr_intersect(nbr_list[*k],nbr_list[*l]) >= m)
˜˜˜˜˜˜˜˜ ^˜
cluster.cc:182:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(nbr_intersect(nbr_list[*k],nbr_list[*l]) >= m)
˜˜˜˜˜˜˜˜ ^˜
cluster.cc:200:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator k = cluster_members[si].begin(); k != cluster_members[si].end(); k++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:200:82: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator k = cluster_members[si].begin(); k != cluster_members[si].end(); k++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:202:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator l = cluster_members[sj].begin(); l != cluster_members[sj].end(); l++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:202:83: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(list<int>::iterator l = cluster_members[sj].begin(); l != cluster_members[sj].end(); l++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
cluster.cc:205:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(nbr_intersect(nbr_list[*k],nbr_list[*l]) < m)
˜˜˜˜˜˜˜˜ ^˜
cluster.cc:205:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(nbr_intersect(nbr_list[*k],nbr_list[*l]) < m)
˜˜˜˜˜˜˜˜ ^˜
cluster.cc:217:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cluster_members[newRep].splice(cluster_members[newRep].end(),cluster_members[otherRep]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
cluster.cc:217:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cluster_members[newRep].splice(cluster_members[newRep].end(),cluster_members[otherRep]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
cluster.cc:217:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cluster_members[newRep].splice(cluster_members[newRep].end(),cluster_members[otherRep]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
cluster.cc:172:88: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int minPairsNeeded = (cluster_members[si].size() * cluster_members[sj].size() + 1 ) / 2;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
cluster.cc:249:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if( ! nbr_list[i].empty())
˜˜˜˜˜˜˜˜ ^
cluster.cc:267:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int j = 0; j < nbr_list[i].size(); j ++) {
˜˜˜˜˜˜˜˜ ^
cluster.cc:268:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!bothDirections || contains(i,nbr_list[j]))
˜˜˜˜˜˜˜˜ ^
cluster.cc:269:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
checkPair(s,i,nbr_list[i][j],m,linkage);
˜˜˜˜˜˜˜˜ ^
cluster.cc:269:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
checkPair(s,i,nbr_list[i][j],m,linkage);
˜˜˜˜˜˜˜˜ ^
cluster.cc:277:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return cluster(names.size(),m,0,SINGLE);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
cluster.cc:289:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int n=INTEGER(neighbors)[j*N+i];
˜^˜˜
cluster.cc:392:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER(result)[i]=s.FindSet(i)+1;
˜ ^
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
^
37 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c desc.cc -o desc.o
In file included from desc.cc:6:
In file included from ./desc.h:21:
./debug.h:9:25: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define DEBUG_PRINT(fmt,...)
^
desc.cc:14:25: warning: implicit conversion loses integer precision: 'unsigned int' to 'char' [-Wconversion]
char bond_order = b->GetBondOrder();
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
desc.cc:82:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
atoms[c - 1] = mol.GetAtom (c);
˜˜˜ ^
desc.cc:92:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (mol.GetBond (i + 1, j + 1) == NULL)
˜˜˜ ˜˜^˜˜
desc.cc:92:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (mol.GetBond (i + 1, j + 1) == NULL)
˜˜˜ ˜˜^˜˜
desc.cc:144:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int ret = _core(mol, descriptors);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
desc.cc:146:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return ret;
˜˜˜˜˜˜ ^˜˜
desc.cc:151:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int ret = calc_desc(mol, descs);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
desc.cc:153:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return ret;
˜˜˜˜˜˜ ^˜˜
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c formats.cc -o formats.o
In file included from formats.cc:1:
In file included from ./desc.h:21:
./debug.h:9:25: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define DEBUG_PRINT(fmt,...)
^
formats.cc:155:16: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
Atom a(line - 4, i);
˜ ˜˜˜˜˜^˜˜
formats.cc:155:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
Atom a(line - 4, i);
˜ ^
formats.cc:188:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
Atom* a1 = mol.GetAtom(left);
˜˜˜ ^˜˜˜
formats.cc:189:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
Atom* a2 = mol.GetAtom(right);
˜˜˜ ^˜˜˜˜
formats.cc:198:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return mol.add_bond(*a1, *a2, bond_type);
˜˜˜ ^˜˜˜˜˜˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c molecule.cc -o molecule.o
molecule.cc:118:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
return atoms.size();
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
molecule.cc:147:8: warning: implicit conversion changes signedness: 'int' to 'const key_type' (aka 'const unsigned int') [-Wsign-conversion]
bonds[key] = b;
˜˜˜˜˜ ^˜˜
molecule.cc:149:28: warning: implicit conversion changes signedness: 'int' to 'const key_type' (aka 'const unsigned int') [-Wsign-conversion]
_a1.register_bond(&(bonds[key]));
˜˜˜˜˜ ^˜˜
molecule.cc:150:28: warning: implicit conversion changes signedness: 'int' to 'const key_type' (aka 'const unsigned int') [-Wsign-conversion]
_a2.register_bond(&(bonds[key]));
˜˜˜˜˜ ^˜˜
molecule.cc:171:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
key = (a1 << 16) + a2;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
molecule.cc:173:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
key = (a2 << 16) + a1;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c r_wrap.cc -o r_wrap.o
r_wrap.cc:654:23: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
uu = ((d - '0') << 4);
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜
r_wrap.cc:656:28: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
uu = ((d - ('a'-10)) << 4);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
r_wrap.cc:680:36: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (strlen(name) + 1 > (bsz - (r - buff))) return 0;
˜ ˜˜^˜˜˜˜˜
r_wrap.cc:1275:95: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
*cptr = reinterpret_cast< char* >(memcpy((new char[len + 1]), cstr, sizeof(char)*(len + 1)));
˜ ˜˜˜˜^˜˜
r_wrap.cc:1281:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*cptr = reinterpret_cast< char * >(malloc(len + 1));
˜˜˜˜˜˜ ˜˜˜˜^˜˜
r_wrap.cc:1284:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (psize) *psize = len + 1;
˜ ˜˜˜˜^˜˜
r_wrap.cc:1271:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(cstr);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
r_wrap.cc:1364:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1400:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1436:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1472:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1507:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1533:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1558:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1594:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(r_nprotect) Rf_unprotect(r_nprotect);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
r_wrap.cc:1685:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
16 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c script.cc -o script.o
In file included from script.cc:2:
In file included from ./desc.h:21:
./debug.h:9:25: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define DEBUG_PRINT(fmt,...)
^
script.cc:23:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int ret = calc_desc(*mol, descs);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
script.cc:33:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int ret = calc_desc(*mol, descs);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
script.cc:43:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int ret = calc_desc(*mol, descs);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
script.cc:56:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
return descs.size();
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DNO_MAIN -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c similarity.cc -o similarity.o
In file included from similarity.cc:1:
In file included from ./desc.h:21:
./debug.h:9:25: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define DEBUG_PRINT(fmt,...)
^
1 warning 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 ChemmineR.so DisjointSets.o cluster.o desc.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'as.vector' from package 'base' in package 'ChemmineR'
Creating a generic function for 'as.matrix' from package 'base' in package 'ChemmineR'
Creating a generic function for 'plot' from package 'graphics' in package 'ChemmineR'
Creating a generic function for 'print' from package 'base' in package 'ChemmineR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)