GLAD 2.24.0
Philippe Hupe
| 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/GLAD | | 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/GLAD.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 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '2.24.0'
* 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 'GLAD' can be installed ... [9s/10s] 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
File 'GLAD/R/zzz.R':
.onLoad calls:
packageStartupMessage("\n")
packageStartupMessage("######################################################################################\n")
packageStartupMessage("\n")
packageStartupMessage("Have fun with GLAD\n")
packageStartupMessage("\n")
packageStartupMessage("For smoothing it is possible to use either\n")
packageStartupMessage("the AWS algorithm (Polzehl and Spokoiny, 2002)\n")
packageStartupMessage("or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008)\n")
packageStartupMessage("\n")
packageStartupMessage("If you use the package with AWS, please cite:\n")
packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)\n")
packageStartupMessage("\n")
packageStartupMessage("If you use the package with HaarSeg, please cite:\n")
packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)\n")
packageStartupMessage("\n")
packageStartupMessage("For fast computation it is recommanded to use\n")
packageStartupMessage("the daglad function with smoothfunc=haarseg\n")
packageStartupMessage("\n")
packageStartupMessage("######################################################################################\n")
packageStartupMessage("\n")
packageStartupMessage("New options are available in daglad: see help for details.")
packageStartupMessage("\n")
See section 'Good practice' in '?.onAttach'.
arrayPersp.arrayCGH: warning in layout(matrix(c(1, 2), 1, 2), width =
c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nc' to 'ncol'
arrayPersp.default: warning in layout(matrix(c(1, 2), 1, 2), width =
c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nc' to 'ncol'
chrBreakpoints.profileCGH: no visible global function definition for
'laws'
chrBreakpoints.profileCGH: possible error in aws(y =
subsetdata[["LogRatio"]], x = x, hinit = hinit, hmax = hmax, sigma2 =
sigma, NN = FALSE, symmetric = TRUE, ...): unused arguments (x = x,
hinit = hinit, NN = FALSE, symmetric = TRUE)
chrBreakpoints.profileCGH: possible error in aws(y =
subsetdata[["LogRatio"]], hinit = hinit, hmax = hmax, sigma2 = sigma,
symmetric = TRUE, ...): unused arguments (hinit = hinit, symmetric =
TRUE)
* 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 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/GLAD.Rcheck/GLAD/libs/GLAD.so':
Found '__ZSt4cout', possibly from 'std::cout' (C++)
Object: 'glad-utils.o'
Found '_printf', possibly from 'printf' (C)
Objects: 'OutliersGNL.o', 'chrBreakpoints.o', 'findCluster.o',
'glad-utils.o', 'hclust.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 ... [8s/8s] 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 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/GLAD.Rcheck/00check.log'
for details.
* installing *source* package 'GLAD' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars
src/Makevars file
PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm
PKG_CPPFLAGS += -DIS_MAC_OS
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BkpInfo.cpp -o BkpInfo.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c HaarSeg.cpp -o HaarSeg.o
HaarSeg.cpp:421:40: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
convResult_tmp1 = (double *)calloc(size, sizeof(double));
˜˜˜˜˜˜ ^˜˜˜
HaarSeg.cpp:422:34: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
peakLoc_tmp1 = (int *)calloc(size, sizeof(double));
˜˜˜˜˜˜ ^˜˜˜
HaarSeg.cpp:423:32: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
uniPeakLoc = (int *)calloc(size, sizeof(double));
˜˜˜˜˜˜ ^˜˜˜
HaarSeg.cpp:424:32: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmpPeakLoc = (int *)calloc(size, sizeof(double));
˜˜˜˜˜˜ ^˜˜˜
HaarSeg.cpp:475:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fdr_tmp1 = (double *)malloc((indice + 1) * sizeof(double));
˜˜˜˜˜˜˜^˜˜ ˜
HaarSeg.cpp:488:33: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memcpy(tmpPeakLoc, uniPeakLoc, size * sizeof(int));
^˜˜˜ ˜
HaarSeg.cpp:515:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
breakpoints = (int *)calloc((indice + 1), sizeof(int));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
HaarSeg.cpp:573:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
p = 2 - 2 * gsl_cdf_gaussian_P (sortedX[i], sdev);
˜˜˜˜˜˜˜ ^
HaarSeg.cpp:587:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return sortedX[k];
˜˜˜˜˜˜˜ ^
HaarSeg.cpp:606:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
st = (int *)malloc((length_peaks + 1) * sizeof(int));
˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜ ˜
HaarSeg.cpp:608:27: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memcpy(&st[1], peaks, length_peaks * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜ ˜
HaarSeg.cpp:610:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ed = (int *)malloc((length_peaks + 1) * sizeof(int));
˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜ ˜
12 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c MoveBkp.cpp -o MoveBkp.o
MoveBkp.cpp:117:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
zone = (int *)malloc(*l * sizeof(int));
^˜ ˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c OutliersGNL.cpp -o OutliersGNL.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c chrBreakpoints.cpp -o chrBreakpoints.o
chrBreakpoints.cpp:107:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
convResult = (double *)calloc(size, sizeof(double));
˜˜˜˜˜˜ ^˜˜˜
chrBreakpoints.cpp:108:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
peakLoc = (int *)calloc(size, sizeof(int));
˜˜˜˜˜˜ ^˜˜˜
chrBreakpoints.cpp:78:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
sizeChr[i] = it_LogRatio_byChr->second.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
chrBreakpoints.cpp:202:29: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
rupture = (int *)calloc(nb, sizeof(int));
˜˜˜˜˜˜ ^˜
chrBreakpoints.cpp:326:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(Breakpoints, &rupture[1], (nb - 1) * sizeof(int)); // <-> subsetdata$Breakpoints <- c(awsBkp$rupture[2:l],0)
˜˜˜^˜˜ ˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cutree.cpp -o cutree.o
cutree.cpp:144:26: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sing = (int *)calloc(n, sizeof(int));
˜˜˜˜˜˜ ^
cutree.cpp:146:26: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
m_nr = (int *)calloc(n, sizeof(int));
˜˜˜˜˜˜ ^
cutree.cpp:148:23: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
z = (int *)calloc(n, sizeof(int));
˜˜˜˜˜˜ ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c daglad.cpp -o daglad.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c distance.cpp -o distance.o
distance.cpp:130:5: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
if(x[i1] || x[i2]){
^˜˜˜˜ ˜˜
distance.cpp:130:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
if(x[i1] || x[i2]){
˜˜ ^˜˜˜˜
distance.cpp:132:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
if( ! (x[i1] && x[i2]) ) dist++;
^˜˜˜˜ ˜˜
distance.cpp:132:20: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
if( ! (x[i1] && x[i2]) ) dist++;
˜˜ ^˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c filterBkp.cpp -o filterBkp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c findCluster.cpp -o findCluster.o
findCluster.cpp:97:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
x_Mean = (double *)malloc(NBR * sizeof(double));
^˜˜ ˜
findCluster.cpp:98:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
members = (double *)malloc(NBR * sizeof(double));
^˜˜ ˜
findCluster.cpp:99:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
clusterRegion_Region = (int *)malloc(NBR * sizeof(int));
^˜˜ ˜
findCluster.cpp:129:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dist = (double *)calloc(taille, sizeof(double));
˜˜˜˜˜˜ ^˜˜˜˜˜
findCluster.cpp:141:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ia = (int *)calloc(NBR, sizeof(int));
˜˜˜˜˜˜ ^˜˜
findCluster.cpp:142:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ib = (int *)calloc(NBR, sizeof(int));
˜˜˜˜˜˜ ^˜˜
findCluster.cpp:143:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
order = (int *)calloc(NBR, sizeof(int));
˜˜˜˜˜˜ ^˜˜
findCluster.cpp:144:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
crit = (double *)calloc(NBR, sizeof(double));
˜˜˜˜˜˜ ^˜˜
findCluster.cpp:164:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
treemerge = (int *)malloc((2 * NBR - 2) * sizeof(int));
˜˜˜˜˜˜˜˜^˜˜ ˜
findCluster.cpp:165:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(&treemerge[0], &ia[0], (NBR - 1) * sizeof(int));
˜˜˜˜^˜˜ ˜
findCluster.cpp:166:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(&treemerge[NBR - 1], &ib[0], (NBR - 1) * sizeof(int));
˜˜˜˜^˜˜ ˜
findCluster.cpp:181:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
classe = (int *)malloc(NBR * sizeof(int));
^˜˜ ˜
findCluster.cpp:264:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
classe = (int *) malloc(NBR * sizeof(int));
^˜˜ ˜
findCluster.cpp:303:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vec_deltaoversigma.push_back(fabs(vec_Mean[j] - vec_Mean[j - 1]) / sigma);
˜˜˜˜˜˜˜˜ ^
findCluster.cpp:303:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vec_deltaoversigma.push_back(fabs(vec_Mean[j] - vec_Mean[j - 1]) / sigma);
˜˜˜˜˜˜˜˜ ˜˜^˜˜
findCluster.cpp:319:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_kernelpen += kernelpen(vec_deltaoversigma[j], d);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
findCluster.cpp:348:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(min_logLike == vec_logLike[i])
˜˜˜˜˜˜˜˜˜˜˜ ^
17 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c glad-utils.cpp -o glad-utils.o
glad-utils.cpp:511:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
diffvalue = vec[i] - vec[i - 1];
˜˜˜ ^
glad-utils.cpp:511:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
diffvalue = vec[i] - vec[i - 1];
˜˜˜ ˜˜^˜˜
glad-utils.cpp:550:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
value_left = vec[(int)(lo)];
˜˜˜ ^˜˜˜˜˜˜˜˜
glad-utils.cpp:563:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
value_right = vec[(int)(hi)];
˜˜˜ ^˜˜˜˜˜˜˜˜
glad-utils.cpp:625:25: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> vaux(vsize);
˜˜˜˜ ^˜˜˜˜
glad-utils.cpp:631:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vaux[i]=fabs(vec[i]-median);
˜˜˜˜ ^
glad-utils.cpp:631:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vaux[i]=fabs(vec[i]-median);
˜˜˜ ^
glad-utils.cpp:624:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const int' [-Wshorten-64-to-32]
const int vsize=vec.size();
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
glad-utils.cpp:646:25: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> vaux(vsize);
˜˜˜˜ ^˜˜˜˜
glad-utils.cpp:655:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aux = vec[i] - mean;
˜˜˜ ^
glad-utils.cpp:645:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const int' [-Wshorten-64-to-32]
const int vsize=vec.size();
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c hclust.cpp -o hclust.o
hclust.cpp:59:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
nn = (int*) malloc (*n * sizeof(int));
^˜ ˜
hclust.cpp:60:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
disnn = (double*) malloc (*n * sizeof(double));
^˜ ˜
hclust.cpp:61:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
flag = (short int*) malloc (*n * sizeof(short int));
^˜ ˜
hclust.cpp:252:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
iia = (int*) malloc (*n * sizeof(int));
^˜ ˜
hclust.cpp:253:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
iib = (int*) malloc (*n * sizeof(int));
^˜ ˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c laws.c -o laws.o
laws.c:33:6: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ih=*hinit;
˜^˜˜˜˜˜
laws.c:52:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
iz=z;
˜^
laws.c:107:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
iz=z;
˜^
laws.c:116:8: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
iz=z;
˜^
laws.c:161:6: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ih=hakt;
˜^˜˜˜
laws.c:171:20: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memcpy(biold,bi,(n_aux*sizeof(bi[0])));
^˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
laws.c:171:20: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memcpy(biold,bi,(n_aux*sizeof(bi[0])));
^˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
laws.c:178:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ih=hakt;
˜^˜˜˜
laws.c:189:24: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memcpy(biold,bi,(n_aux*sizeof(bi[0])));
^˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
laws.c:189:24: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memcpy(biold,bi,(n_aux*sizeof(bi[0])));
^˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
10 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c loopRemove.cpp -o loopRemove.o
loopRemove.cpp:129:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux.push_back(aggTot[j]);
˜˜˜˜˜˜ ^
loopRemove.cpp:133:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux[i].Card = aggTot[i].Card + aggTot[indRegion].Card;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:133:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux[i].Card = aggTot[i].Card + aggTot[indRegion].Card;
˜˜˜˜˜˜ ^
loopRemove.cpp:133:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux[i].Card = aggTot[i].Card + aggTot[indRegion].Card;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:134:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
barycentre = aggTot[i].Card*aggTot[i].Mean + aggTot[indRegion].Card*aggTot[indRegion].Mean;
˜˜˜˜˜˜ ^
loopRemove.cpp:134:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
barycentre = aggTot[i].Card*aggTot[i].Mean + aggTot[indRegion].Card*aggTot[indRegion].Mean;
˜˜˜˜˜˜ ^
loopRemove.cpp:134:69: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
barycentre = aggTot[i].Card*aggTot[i].Mean + aggTot[indRegion].Card*aggTot[indRegion].Mean;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:134:92: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
barycentre = aggTot[i].Card*aggTot[i].Mean + aggTot[indRegion].Card*aggTot[indRegion].Mean;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:135:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
barycentre = barycentre / aggTotAux[i].Card;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:136:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux[i].Mean = barycentre;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:137:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
within = aggTot[i].Card * aggTot[i].Var + aggTot[indRegion].Card * aggTot[indRegion].Var;
˜˜˜˜˜˜ ^
loopRemove.cpp:137:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
within = aggTot[i].Card * aggTot[i].Var + aggTot[indRegion].Card * aggTot[indRegion].Var;
˜˜˜˜˜˜ ^
loopRemove.cpp:137:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
within = aggTot[i].Card * aggTot[i].Var + aggTot[indRegion].Card * aggTot[indRegion].Var;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:137:91: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
within = aggTot[i].Card * aggTot[i].Var + aggTot[indRegion].Card * aggTot[indRegion].Var;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:138:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
within = within / aggTotAux[i].Card;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:139:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
between = aggTot[i].Card * (aggTot[i].Mean-barycentre) * (aggTot[i].Mean-barycentre);
˜˜˜˜˜˜ ^
loopRemove.cpp:139:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
between = aggTot[i].Card * (aggTot[i].Mean-barycentre) * (aggTot[i].Mean-barycentre);
˜˜˜˜˜˜ ^
loopRemove.cpp:139:68: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
between = aggTot[i].Card * (aggTot[i].Mean-barycentre) * (aggTot[i].Mean-barycentre);
˜˜˜˜˜˜ ^
loopRemove.cpp:140:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
between += aggTot[indRegion].Card * (aggTot[indRegion].Mean-barycentre) * (aggTot[indRegion].Mean-barycentre);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:140:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
between += aggTot[indRegion].Card * (aggTot[indRegion].Mean-barycentre) * (aggTot[indRegion].Mean-barycentre);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:140:85: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
between += aggTot[indRegion].Card * (aggTot[indRegion].Mean-barycentre) * (aggTot[indRegion].Mean-barycentre);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:141:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
between = between / aggTotAux[i].Card;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:142:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux[i].Var = within + between;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:143:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux[i].VarLike=aggTotAux[i].Var;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:143:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
aggTotAux[i].VarLike=aggTotAux[i].Var;
˜˜˜˜˜˜˜˜˜ ^
loopRemove.cpp:151:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
LabelRegionRemoved = aggTot[i].LabelRegion;
˜˜˜˜˜˜ ^
loopRemove.cpp:152:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
LabelRegionRemovedNext = aggTot[indRegion].LabelRegion;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
loopRemove.cpp:88:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
agg_aux.Card = it_LogRatio->second.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
loopRemove.cpp:114:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
nbregion = aggTot.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
loopRemove.cpp:472:30: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
LevelAux = (int *)malloc(n * sizeof(int));
^ ˜
loopRemove.cpp:496:29: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memcpy(Level, LevelAux, n * sizeof(int));
^ ˜
31 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 GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GLAD.Rcheck/GLAD/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GLAD)