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Package 644/671HostnameOS / ArchBUILDCHECKBUILD BIN
triplex 1.0.7
Jiri Hon
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/triplex
Last Changed Rev: 76143 / Revision: 76155
Last Changed Date: 2013-04-30 03:04:31 -0700 (Tue, 30 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 

Summary

Package: triplex
Version: 1.0.7
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch triplex_1.0.7.tar.gz
StartedAt: 2013-05-01 11:34:15 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:37:14 -0700 (Wed, 01 May 2013)
EllapsedTime: 179.4 seconds
RetCode: 0
Status:  OK 
CheckDir: triplex.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/triplex.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 'triplex/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'triplex' version '1.0.7'
* 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 'triplex' can be installed ... [19s/20s] 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 ... [9s/9s] 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

triplex.Rcheck/00install.out:

* installing *source* package 'triplex' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_triplex.c -o R_init_triplex.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c align.c -o align.o
align.c:53:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        seq_l = strlen(seq);
              ˜ ^˜˜˜˜˜˜˜˜˜˜
align.c:136:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                body1[i1++] = toupper(nukl2char(seq[seq_l-1-row]));
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align.c:137:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                                body2[i2++] = toupper(nukl2char(seq[col]));
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align.c:262:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        t_diag** mat = (t_diag**)malloc(size*sizeof(t_diag*));  
                                        ^˜˜˜˜
align.c:270:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                mat[x] = (t_diag*)malloc(size*sizeof(t_diag));      
                                         ^˜˜˜˜
align.c:360:28: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
                        diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
align.c:360:38: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
                        diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c align_interface.c -o align_interface.o
align_interface.c:47:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .tri_type = t[0],
                            ^˜˜˜
align_interface.c:48:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .min_score = p[P_MIN_SCORE],
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:50:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .min_len = p[P_MIN_LEN],
                           ^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:51:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .max_len = p[P_MAX_LEN],
                           ^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:52:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .min_loop = p[P_MIN_LOOP],
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:53:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .max_loop = p[P_MAX_LOOP],
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:58:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .dtwist = p[P_DTWIST_PEN],
                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:62:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .mismatch = p[P_MIS_PEN] 
                            ^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:59:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .insertion = p[P_INS_PEN],
                             ^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:60:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .iso_change = p[P_ISO_PEN],
                              ^˜˜˜˜˜˜˜˜˜˜˜
align_interface.c:61:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .iso_stay = p[P_ISO_BONUS],
                            ^˜˜˜˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c dl_list.c -o dl_list.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c libtriplex.c -o libtriplex.o
libtriplex.c:262:7: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        ch = tolower(ch);
           ˜ ^˜˜˜˜˜˜˜˜˜˜
libtriplex.c:406:36: warning: implicit conversion changes signedness: 'int' to 'unsigned char' [-Wsign-conversion]
        unsigned char i = 0, j = 0, max = - 99, tmp;
                                    ˜˜˜   ^˜˜˜
libtriplex.c:410:10: warning: implicit conversion loses integer precision: 'const int' to 'unsigned char' [-Wconversion]
                        tmp = tab_score[triplex_type][n1[i]][n2[j]];
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
libtriplex.c:419:10: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
                                *a = n1[i];
                                   ˜ ^˜˜˜˜
libtriplex.c:420:10: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
                                *b = n2[j];
                                   ˜ ^˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c progress.c -o progress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c search.c -o search.o
search.c:86:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                int pieces = ceil(chunk_l / (double) params.max_chunk_size);
                    ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
search.c:71:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                int chunk_l = strlen(chunk);
                    ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
search.c:80:28: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                int chunk_offset = chunk - dna.seq;
                    ˜˜˜˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
search.c:101:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                        int piece_offset = piece - chunk;
                            ˜˜˜˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜˜
search.c:283:28: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
                        diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
search.c:283:38: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
                        diag[d] = get_max_score(piece[i], piece[i-x], diag[d-1], diag[d], diag[d+1], d, x, params->tri_type, params->max_loop, pen);
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c search_interface.c -o search_interface.o
search_interface.c:50:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                dna.seq[i] = tolower(DNAdecode(x.seq[i]));
                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:218:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .min_score = p[P_MIN_SCORE],
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:220:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .min_len = p[P_MIN_LEN],
                           ^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:221:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .max_len = p[P_MAX_LEN],
                           ^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:222:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .min_loop = p[P_MIN_LOOP],
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:223:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .max_loop = p[P_MAX_LOOP],
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:229:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .dtwist = p[P_DTWIST_PEN],
                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:233:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .mismatch = p[P_MIS_PEN]
                            ^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:230:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .insertion = p[P_INS_PEN],
                             ^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:231:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .iso_change = p[P_ISO_PEN],
                              ^˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:232:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                .iso_stay = p[P_ISO_BONUS],
                            ^˜˜˜˜˜˜˜˜˜˜˜˜˜
search_interface.c:246:45: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                dl_list_init(&dl_list_arr[i], p[P_MAX_LEN]+p[P_MAX_LOOP]); // FIXME
                ˜˜˜˜˜˜˜˜˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
12 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 triplex.so Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o align.o align_interface.o dl_list.o libtriplex.o progress.o search.o search_interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/triplex.Rcheck/triplex/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (triplex)

triplex.Rcheck/triplex-Ex.timings:

nameusersystemelapsed
TriplexViews-class0.7460.0290.780
ins0.0400.0030.042
lend0.0430.0040.048
lstart0.0450.0030.049
lwidth0.0420.0030.045
pvalue0.0370.0020.040
triplex-package0.1400.0050.146
triplex.3D0.0380.0010.039
triplex.alignment0.1020.0040.106
triplex.diagram0.1080.0030.111
triplex.search0.1970.0050.202