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Package 641/671HostnameOS / ArchBUILDCHECKBUILD BIN
TransView 1.4.2
Julius Muller
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/TransView
Last Changed Rev: 75930 / Revision: 76155
Last Changed Date: 2013-04-23 00:54:55 -0700 (Tue, 23 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: TransView
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TransView_1.4.2.tar.gz
StartedAt: 2013-05-01 11:32:09 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:35:51 -0700 (Wed, 01 May 2013)
EllapsedTime: 222.2 seconds
RetCode: 0
Status:  OK 
CheckDir: TransView.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/TransView.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 'TransView/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TransView' version '1.4.2'
* 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 'TransView' can be installed ... [20s/21s] 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 compilation flags in Makevars ... 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 ... [22s/22s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'TransView_unit_tests.R' [18s/18s]
 [19s/19s] 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

TransView.Rcheck/00install.out:

* installing *source* package 'TransView' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_TransView.c -o R_init_TransView.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bin_density.c -o bin_density.o
bin_density.c:32:6: warning: unused variable 'msum' [-Wunused-variable]
        int msum=0,result=orivec[*cpos];
            ^
bin_density.c:64:75: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        return((orivec[*cpos-(wwidth/2)-1] + orivec[*cpos-((wwidth-1)/2)-1]) / 2.0);
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
bin_density.c:102:30: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int msum,mpos,cpos=0,wwidth=ceil((double)orivecl/(double)window_count),nvc=0;
                             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bin_density.c:102:11: warning: unused variable 'mpos' [-Wunused-variable]
        int msum,mpos,cpos=0,wwidth=ceil((double)orivecl/(double)window_count),nvc=0;
                 ^
bin_density.c:102:6: warning: unused variable 'msum' [-Wunused-variable]
        int msum,mpos,cpos=0,wwidth=ceil((double)orivecl/(double)window_count),nvc=0;
            ^
bin_density.c:124:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int wwidth=floor((double)window_count/(double)orivecl),cpos=0,wc=0,nvc=0;
            ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bin_density.c:153:9: warning: unused variable 'msum' [-Wunused-variable]
        double msum=0,result=orivec[*cpos];
               ^
bin_density.c:224:30: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int msum,mpos,cpos=0,wwidth=ceil((double)orivecl/(double)window_count),nvc=0;
                             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bin_density.c:224:11: warning: unused variable 'mpos' [-Wunused-variable]
        int msum,mpos,cpos=0,wwidth=ceil((double)orivecl/(double)window_count),nvc=0;
                 ^
bin_density.c:224:6: warning: unused variable 'msum' [-Wunused-variable]
        int msum,mpos,cpos=0,wwidth=ceil((double)orivecl/(double)window_count),nvc=0;
            ^
bin_density.c:246:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int wwidth=floor((double)window_count/(double)orivecl),cpos=0,wc=0,nvc=0;
            ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c construct_dc.c -o construct_dc.o
In file included from construct_dc.c:23:
In file included from ./parse_sam.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                data = (uint8_t*)realloc(data, m_data);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        b->data = (uint8_t*)calloc(b->data_len, 1);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
construct_dc.c:40:9: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        return(fcvg);
        ˜˜˜˜˜˜ ^˜˜˜
construct_dc.c:71:11: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ft->seqn=flen;
                ˜^˜˜˜
construct_dc.c:176:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        chrom_tid=bresults.chrom_index_next;
                 ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:177:103: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        if(user_args->VERBOSE>0)printStatus(bam_file->header->target_name[chrom_tid], &cc, bam_file->header->n_targets);
                                ˜˜˜˜˜˜˜˜˜˜˜                                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
construct_dc.c:180:104: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                if(user_args->VERBOSE>0)printStatus(bam_file->header->target_name[chrom_tid], &cc, bam_file->header->n_targets);
                                        ˜˜˜˜˜˜˜˜˜˜˜                                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
construct_dc.c:185:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                cs.max_pos=bam_file->header->target_len[chrom_tid]+1;//+1 for 0 based sources
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
construct_dc.c:188:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                gd->gsize+=cs.min_scorespace;//calculate total amount of genomic region covered [spanning first read to last read]
                         ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:208:24: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                chrom_tid=bresults.chrom_index_next;
                                         ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:215:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        cs.min_scorespace=filter_coverage(filter_index,ft);//override scorespace by bps covered by the filter
                                         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:236:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                cs.min_scorespace=(++cs.min_scorespace)/(4/sizeof(usersize));//Only half the space needed with uint16_t
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
construct_dc.c:257:12: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                bstart=ft->values[filter_index][fcount++];//C index 0 based
                                      ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:258:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                bend=ft->values[filter_index][fcount++];//C index 0 based
                                    ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:261:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        if(fcount>3)bend=ft->values[filter_index][fcount-3];//just in case the end of the chromosome is reached -> use last end as index end
                                                        ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:269:31: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        gen_indp[scount_ind]=bstart+1;//C index 0 based -> genomic position +1
                                            ˜˜˜˜˜˜˜^˜
construct_dc.c:270:23: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        l_indp[scount_ind]=scount;//R index 1 based -> but accession will be in C
                                          ˜^˜˜˜˜˜
construct_dc.c:282:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                        if(histc%user_args->HWINDOW==0){
                                                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
construct_dc.c:283:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                                ++gd->histogramp[windowt/user_args->HWINDOW];
                                                                        ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
construct_dc.c:292:64: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        if(user_args->HWINDOW>1)++gd->histogramp[windowt/user_args->HWINDOW];//empty last window | prerequisite: HWINDOW<=COMPRESSION!
                                                                        ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
construct_dc.c:298:48: warning: operand of ? changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                gen_indp[scount_ind]=user_args->FILTER ? bend+1 : cs.max_pos+1;//override read based cs.maxpos to filter end in case of FILTER. +1 to indicate start of next block
                                    ˜                    ˜˜˜˜^˜
construct_dc.c:299:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                l_indp[scount_ind]=scount;
                                  ˜^˜˜˜˜˜
construct_dc.c:329:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                chrom_tid=bresults.chrom_index_next;
                         ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:402:13: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                UNPROTECT(upcounter);
                ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:548:35: note: expanded from macro 'UNPROTECT'
#define UNPROTECT(n)    Rf_unprotect(n)
                                     ^
construct_dc.c:415:38: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        gd.total_elements=bam_file->header->n_targets;//one vector per chromosome needed
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
construct_dc.c:419:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        upcounter+=set_filter(filterList,&ft);
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
construct_dc.c:467:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    UNPROTECT(upcounter+gd.upcounter);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:548:35: note: expanded from macro 'UNPROTECT'
#define UNPROTECT(n)    Rf_unprotect(n)
                                     ^
27 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c parse_sam.c -o parse_sam.o
In file included from parse_sam.c:13:
In file included from ./parse_sam.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                data = (uint8_t*)realloc(data, m_data);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        b->data = (uint8_t*)calloc(b->data_len, 1);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
parse_sam.c:75:23: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
        bufread->revcomp=rm->revcomp;
                        ˜˜˜˜˜^˜˜˜˜˜˜
parse_sam.c:115:19: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        rm->genomic_end= bam_calend(&temp_read->core,bam1_cigar(temp_read));
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
parse_sam.c:150:13: warning: implicit conversion changes signedness: 'int' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                        rm->skip=-4;
                                ˜^˜
parse_sam.c:162:13: warning: implicit conversion changes signedness: 'int' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
                        rm->skip=-4;
                                ˜^˜
parse_sam.c:192:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
                bresults->mapmass+=rm->read_length;
                                 ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
parse_sam.c:235:54: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        uint32_t nindex=0,*ind_start,*ind_end,max_index=cs->min_indexspace;
                                              ˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
parse_sam.c:243:34: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        uint32_t BUFFERLIMIT=cs->max_pos+1;//there are no more than this many items calloc'ed
                 ˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
parse_sam.c:244:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        uint32_t INDEXLIMIT=cs->min_indexspace;
                 ˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
parse_sam.c:262:24: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        *(databl_end++)=cs->max_pos;//completes the missing end entry to be on par with start
                                       ˜˜˜˜˜^˜˜˜˜˜˜
parse_sam.c:265:23: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        cs->min_indexspace=nindex;
                                          ˜^˜˜˜˜˜
parse_sam.c:294:23: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                *databl_end++=cs->max_pos;//completes the missing end entry to be on par with start
                                             ˜˜˜˜˜^˜˜˜˜˜˜
parse_sam.c:296:24: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                                cs->min_indexspace=nindex;
                                                  ˜^˜˜˜˜˜
parse_sam.c:354:48: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        }else{write_density_gapped(cptr,fr.cigar,fr.n_cigar,&bresults.maxScore);}
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜               ˜˜˜^˜˜˜˜˜˜
parse_sam.c:370:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        *databl_start++=fr.pos;++nindex;//genomic coordinate where the data block starts
                                       ˜˜˜˜^˜˜
parse_sam.c:373:23: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        cs->min_indexspace=nindex;
                                          ˜^˜˜˜˜˜
parse_sam.c:390:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        *databl_end++=last_end;//genomic coordinate where the data block ends | lags one index position behind start in the main loop!
                                     ˜^˜˜˜˜˜˜˜
parse_sam.c:392:39: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                        *databl_start++=current_read->core.pos;//genomic coordinate where the data block starts beginning with the current read
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
19 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c slice_dc.c -o slice_dc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c visuals.c -o visuals.o
visuals.c:36:18: warning: implicit conversion turns floating-point number into integer: 'float' to 'int' [-Wconversion]
    int c= ratio * w;
        ˜  ˜˜˜˜˜˜^˜˜
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 TransView.so R_init_TransView.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/TransView.Rcheck/TransView/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 (TransView)

TransView.Rcheck/TransView-Ex.timings:

nameusersystemelapsed
DensityContainer-class0.2990.0110.319
TVResults-class0.0100.0040.014
TransView-package0.0080.0030.011
annotatePeaks0.2590.0200.283
gtf2gr0.1300.0050.136
macs2gr0.0590.0040.063
meltPeak1.2650.4921.873
parseReads0.8470.2911.140
peak2tss0.2470.0370.283
plotTV1.4810.5052.004
plotTVData1.5190.5162.043
rmTV0.8550.2861.157
slice11.4790.5482.077
slice1T1.6740.1341.842