Package: TargetSearch

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TargetSearch_1.16.0.tar.gz

StartedAt: 2013-05-01 11:24:47 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 11:27:08 -0700 (Wed, 01 May 2013)

EllapsedTime: 140.6 seconds

RetCode: 0

Status:  OK

CheckDir: TargetSearch.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/TargetSearch.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 'TargetSearch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TargetSearch' version '1.16.0'
* 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 'TargetSearch' 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 ... 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 ... [47s/49s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
RIcorrect 20.071  1.947  23.321
* 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 'TargetSearch' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c file.c -o file.o
file.c:72:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.ri = (double *) R_alloc(splen, sizeof(double));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:73:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.rt = (double *) R_alloc(splen, sizeof(double));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:74:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.n  = (int *) R_alloc(splen, sizeof(int));
                             ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:75:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.pk = (struct peaks *) R_alloc(splen, sizeof(struct peaks));
                                      ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:77:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        fread(spectra.ri, splen * sizeof(double), 1, fp);
                          ^˜˜˜˜ ˜
file.c:78:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        fread(spectra.rt, splen * sizeof(double), 1, fp);
                          ^˜˜˜˜ ˜
file.c:79:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        fread(spectra.n, splen *  sizeof(int), 1, fp);
                         ^˜˜˜˜ ˜
file.c:87:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.pk[0].mass = (int *) R_alloc(sptotal, sizeof(int));
                                     ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
file.c:88:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.pk[0].in   = (int *) R_alloc(sptotal, sizeof(int));
                                     ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
file.c:95:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                fread(spectra.pk[i].mass, spectra.n[i] * sizeof(int), 1, fp);
                                          ^˜˜˜˜˜˜˜˜˜˜˜ ˜
file.c:96:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                fread(spectra.pk[i].in, spectra.n[i] * sizeof(int), 1, fp);
                                        ^˜˜˜˜˜˜˜˜˜˜˜ ˜
file.c:187:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.ri = (double *) R_alloc(total, sizeof(double));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:188:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.rt = (double *) R_alloc(total, sizeof(double));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:189:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.n  = (int *) R_alloc(total, sizeof(int));
                             ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:190:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        spectra.pk = (struct peaks *) R_alloc(total, sizeof(struct peaks));
                                      ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:209:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                str_alloc(ri_str, ri_len, len);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./file.h:14:52: note: expanded from macro 'str_alloc'
                                x = (char *) R_chk_calloc(len, sizeof(char)); \
                                                          ^
file.c:210:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                str_alloc(rt_str, rt_len, len);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./file.h:14:52: note: expanded from macro 'str_alloc'
                                x = (char *) R_chk_calloc(len, sizeof(char)); \
                                                          ^
file.c:211:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                str_alloc(sp_str, sp_len, len);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./file.h:14:52: note: expanded from macro 'str_alloc'
                                x = (char *) R_chk_calloc(len, sizeof(char)); \
                                                          ^
file.c:243:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                spectra.pk[j].mass = (int *) R_alloc(n , sizeof(int));
                                             ˜˜˜˜˜˜˜ ^
file.c:244:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                spectra.pk[j].in   = (int *) R_alloc(n , sizeof(int));
                                             ˜˜˜˜˜˜˜ ^
file.c:275:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        sp_len = strlen(spectrum);
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
file.c:350:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sp.ri         = (double *) R_alloc(splen, sizeof(double));
                                   ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:351:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sp.rt         = (double *) R_alloc(splen, sizeof(double));
                                   ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:352:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sp.n          = (int *) R_alloc(splen, sizeof(int));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:353:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sp.pk         = (struct peaks *) R_alloc(splen, sizeof(struct peaks));
                                         ˜˜˜˜˜˜˜ ^˜˜˜˜
file.c:354:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sp.pk[0].mass = (int *) R_alloc(sptotal, sizeof(int));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
file.c:355:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sp.pk[0].in   = (int *) R_alloc(sptotal, sizeof(int));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
27 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c find_peaks.c -o find_peaks.o
find_peaks.c:117:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        b = ri[0];
          ˜ ^˜˜˜˜
find_peaks.c:120:26: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        i = (ri_min - b) / m;
          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c getLine.c -o getLine.o
getLine.c:11:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                *line = (char *) R_chk_calloc(*n, sizeof(char));
                                 ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
getLine.c:19:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        *line = (char *) R_chk_realloc(*line, *n * sizeof(char));
                                                              ^˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c hpf.c -o hpf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ncdf.c -o ncdf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c netcdf_peak_finding.c -o netcdf_peak_finding.o
netcdf_peak_finding.c:60:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        diff = (int *) R_alloc( N * (scan_number - 1), sizeof(int));
                       ˜˜˜˜˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
netcdf_peak_finding.c:61:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        x    = (int *) R_alloc( N, sizeof(int));
                       ˜˜˜˜˜˜˜  ^
netcdf_peak_finding.c:62:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        y    = (int *) R_alloc( N, sizeof(int));
                       ˜˜˜˜˜˜˜  ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c peakExtraction.c -o peakExtraction.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ppc.c -o ppc.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o TargetSearch.so Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/TargetSearch.Rcheck/TargetSearch/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 (TargetSearch)

name	user	system	elapsed
FAMEoutliers	0.087	0.016	0.142
FindPeaks	0.692	0.033	0.777
ImportFameSettings	0.030	0.004	0.035
ImportLibrary	0.038	0.006	0.045
ImportSamples	0.026	0.003	0.029
NetCDFPeakFinding	0.990	0.080	1.128
Profile	2.328	0.141	2.493
ProfileCleanUp	2.200	0.090	2.313
RIcorrect	20.071	1.947	23.321
fixRI	2.034	0.272	2.348
medianRILib	1.356	0.058	1.424
peakFind	0.713	0.040	0.759
plotFAME	0.038	0.012	0.052
plotPeak	0.518	0.096	0.630
plotPeakSimple	0.962	0.152	1.144
plotRIdev	1.026	0.061	1.120
plotSpectra	0.727	0.030	0.834
quantMatrix	2.187	0.083	2.327
ri2rt	0.139	0.024	0.163
riMatrix	1.966	0.209	2.216
rt2ri	0.012	0.007	0.019
sampleRI	1.396	0.049	1.475
tsLib-class	0.024	0.023	0.050
tsMSdata-class	0.007	0.007	0.015
tsProfile-class	0.006	0.007	0.013
tsRim-class	0.011	0.015	0.027
tsSample-class	0.050	0.029	0.080
writeLibText	0.063	0.014	0.079