CALIB 1.26.0
Hui Zhao
| 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/CALIB | | 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/CALIB.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 'CALIB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIB' version '1.26.0'
* 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 'CALIB' can be installed ... [10s/12s] 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
read.rg: warning in scan(fullname, what = "", sep = sep, quote = quote,
skip = 1, nlines = 1, quiet = TRUE, allowEscape = FALSE): partial
argument match of 'allowEscape' to 'allowEscapes'
getColClasses: no visible global function definition for 'namesInFun'
plotSpikeCI: no visible binding for global variable 'otherindex'
read.rg: no visible global function definition for 'readBlueFuseHeader'
read.spike: no visible binding for global variable 'files'
* 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 ... [15s/15s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
estimateParameter 8.393 0.06 8.76
* 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 was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/CALIB.Rcheck/00check.log'
for details.
* installing *source* package 'CALIB' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Design.cpp -o Design.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Estimation.cpp -o Estimation.o
Estimation.cpp:144:19: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:25: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:30: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:35: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:40: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:49: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:58: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:67: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:197:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
xspoterror[i] = error[i];
˜˜˜˜˜ ^
Estimation.cpp:192:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'R_len_t' (aka 'int') [-Wshorten-64-to-32]
size = error.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:51:15: note: expanded from macro 'error'
#define error Rf_error
^
Estimation.cpp:223:30: warning: 'readinparlist' has C-linkage specified, but returns incomplete type 'vector<ParameterofOneArray>' which could be incompatible with C [-Wreturn-type-c-linkage]
vector <ParameterofOneArray> readinparlist(SEXP parlist, int ncol)
^
Estimation.cpp:510:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
dataofoneclone = normalizeddata[i];
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
Estimation.cpp:514:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
REAL(result)[i+rnrow*j] = dataofoneclone.Conc[j];
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
Estimation.cpp:548:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
xdimnamescol[i] = condition[i];
˜˜˜˜˜˜˜˜˜ ^
Estimation.cpp:498:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
rnrow = normalizeddata.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Estimation.cpp:499:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
rncol = condition.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
16 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c NormalizedData.cpp -o NormalizedData.o
NormalizedData.cpp:56:20: warning: implicit conversion changes signedness: 'unsigned int' to 'const value_type' (aka 'const int') [-Wsign-conversion]
index.push_back(i);
˜˜˜˜˜ ^
NormalizedData.cpp:84:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inten1_pick.push_back(inten1[*pindex]);
˜˜˜˜˜˜ ^˜˜˜˜˜˜
NormalizedData.cpp:85:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inten2_pick.push_back(inten2[*pindex]);
˜˜˜˜˜˜ ^˜˜˜˜˜˜
NormalizedData.cpp:139:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
index = i;
˜ ^
NormalizedData.cpp:143:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
parameterofone = par[index];
˜˜˜ ^˜˜˜˜
NormalizedData.cpp:149:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
index = i;
˜ ^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ParameterofOneArray.cpp -o ParameterofOneArray.o
In file included from ParameterofOneArray.cpp:4:
./ParameterofOneArray.h:11:9: warning: private field 'SpotErrorofOneSpot' is not used [-Wunused-private-field]
double SpotErrorofOneSpot;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c RawDataofOneArray.cpp -o RawDataofOneArray.o
RawDataofOneArray.cpp:162:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inten2.push_back(Data.Col2Inten[i]);
˜˜˜˜ ^
RawDataofOneArray.cpp:243:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inten1.push_back(Data.Col1Inten[i]);
˜˜˜˜ ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c SpikeofOneArray.cpp -o SpikeofOneArray.o
SpikeofOneArray.cpp:358:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int Stable_Size = int(Stable_Factor * a.size()); // need to discuss about 0.05
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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 CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CALIB.Rcheck/CALIB/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 (CALIB)