R453Plus1Toolbox 1.10.0
Hans-Ulrich Klein
| 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/R453Plus1Toolbox | | 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/R453Plus1Toolbox.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 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.10.0'
* 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 'R453Plus1Toolbox' can be installed ... [43s/45s] 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
.getEnsemblInfo: no visible binding for global variable 'cds_length'
.getEnsemblInfo: no visible binding for global variable
'ensembl_transcript_id'
.getMutations: no visible binding for global variable 'PatternStart'
.getMutations: no visible binding for global variable 'PatternEnd'
.htmlReport: no visible binding for global variable 'VarFreqForward'
.htmlReport: no visible binding for global variable 'VarFreqReverse'
.plotVariants: no visible binding for global variable 'mutation'
qualityReportSFF: no visible binding for '<<-' assignment to 'tmp'
* 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 ... [62s/72s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mergeBreakpoints 15.668 1.371 17.843
htmlReport 7.576 0.489 14.076
plotChimericReads 6.536 0.053 7.949
* 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/R453Plus1Toolbox.Rcheck/00check.log'
for details.
* installing *source* package 'R453Plus1Toolbox' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c readSFF.c -o readSFF.o
readSFF.c:35:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
fileLen = ftell(file);
˜ ^˜˜˜˜˜˜˜˜˜˜
readSFF.c:68:29: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
header->header_len = be_int2(*(uint16_t *)(buffer+24));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:69:29: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
header->key_len = be_int2(*(uint16_t *)(buffer+26));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:70:29: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
header->flow_len = be_int2(*(uint16_t *)(buffer+28));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:128:25: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
pointer = pointer + header->index_len;
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
readSFF.c:128:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
pointer = pointer + header->index_len;
^˜˜˜˜˜˜ ˜
readSFF.c:144:34: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
read->header_len = be_int2(*(uint16_t *)(buffer+pointer+0));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:145:34: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
read->name_len = be_int2(*(uint16_t *)(buffer+pointer+2));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:147:34: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
read->clip_qual_left = be_int2(*(uint16_t *)(buffer+pointer+8));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:148:34: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
read->clip_qual_right = be_int2(*(uint16_t *)(buffer+pointer+10));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:149:34: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
read->clip_adapter_left = be_int2(*(uint16_t *)(buffer+pointer+12));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:150:34: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
read->clip_adapter_right = be_int2(*(uint16_t *)(buffer+pointer+14));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:177:28: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
read->flowgram[k] = be_int2(read->flowgram[k]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
readSFF.c:210:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
pointer = pointer + 2*header->flow_len + 3*read->nbases;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
readSFF.c:210:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
pointer = pointer + 2*header->flow_len + 3*read->nbases;
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c writeSFF.c -o writeSFF.o
writeSFF.c:61:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
uint32_t nreads = be_int4(GET_LENGTH(reads));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:174:20: note: expanded from macro 'be_int4'
#define be_int4(x) iswap_int4((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:119:31: note: expanded from macro 'iswap_int4'
((x & 0x0000ff00) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:61:29: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
uint32_t nreads = be_int4(GET_LENGTH(reads));
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:136:24: note: expanded from macro 'GET_LENGTH'
#define GET_LENGTH(x) length(x)
^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1029:20: note: expanded from macro 'length'
#define length(x) Rf_length(x)
^˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:174:32: note: expanded from macro 'be_int4'
#define be_int4(x) iswap_int4((x))
^
./io_lib/os.h:121:8: note: expanded from macro 'iswap_int4'
((x & 0xff000000) >> 24))
^
writeSFF.c:68:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char* keySequence = R_alloc(kLength, sizeof(char));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
writeSFF.c:70:24: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t keyLength = be_int2(kLength);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:76:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char* flowChars = R_alloc(nFlows, sizeof(char));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
writeSFF.c:78:26: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t numberFlows = be_int2(nFlows);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:87:27: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t headerlength = be_int2(hlength);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:93:36: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
uint8_t flowgramFormat = be_int1(INTEGER(getListElement(ll, "flowgramFormat"))[0]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:176:21: note: expanded from macro 'be_int1'
#define be_int1(x) (x)
^
writeSFF.c:96:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(flowChars, nFlows, 1, file);
˜˜˜˜˜˜ ^˜˜˜˜˜
writeSFF.c:97:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(keySequence, kLength, 1, file);
˜˜˜˜˜˜ ^˜˜˜˜˜˜
writeSFF.c:101:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(&filling, hlength - 31 - kLength - nFlows, 1, file);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
writeSFF.c:131:33: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t readHeaderLength = be_int2(rhlength);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:135:27: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t nameLength = be_int2(strlen(CHAR(STRING_ELT(names, i))));
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:143:32: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t clipQualityLeft = be_int2(INTEGER(cql)[i]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:145:33: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t clipQualityRight = be_int2(INTEGER(cqr)[i]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:147:32: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t clipAdapterLeft = be_int2(INTEGER(cal)[i]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:149:33: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t clipAdapterRight = be_int2(INTEGER(car)[i]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:159:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fwrite(&rh_filling, rhlength - 16 - strlen(CHAR(STRING_ELT(names, i))), 1, file);
˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
writeSFF.c:167:21: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
uint16_t fg = be_int2(flowgram[j]);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:175:20: note: expanded from macro 'be_int2'
#define be_int2(x) iswap_int2((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:124:26: note: expanded from macro 'iswap_int2'
(((x & 0x00ff) << 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
writeSFF.c:174:28: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
uint8_t fi = be_int1(flowIndexes[k]);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:176:21: note: expanded from macro 'be_int1'
#define be_int1(x) (x)
^
writeSFF.c:187:28: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
uint8_t qs = be_int1(qualityScores[l]);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:176:21: note: expanded from macro 'be_int1'
#define be_int1(x) (x)
^
writeSFF.c:193:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fwrite(&rd_filling, 8 - ((3 * strlen(CHAR(STRING_ELT(reads, i))) + 2 * nFlows) % 8), 1, file);
˜ ˜˜^˜˜˜˜˜˜˜
writeSFF.c:67:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int kLength = strlen(CHAR(STRING_ELT(kSequence, 0)));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
writeSFF.c:75:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nFlows = strlen(CHAR(STRING_ELT(fChars, 0)));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
writeSFF.c:125:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int rhlength = 16 + strlen(CHAR(STRING_ELT(names, i)));
˜˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
writeSFF.c:139:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
uint32_t numberBases = be_int4(strlen(CHAR(STRING_ELT(reads, i))));
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:174:20: note: expanded from macro 'be_int4'
#define be_int4(x) iswap_int4((x))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./io_lib/os.h:120:31: note: expanded from macro 'iswap_int4'
((x & 0x00ff0000) >> 8) + \
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
26 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 R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'boxplot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'boxplot' when loading 'graphics'
* DONE (R453Plus1Toolbox)