Starr 1.16.0
Benedikt Zacher
| 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/Starr | | 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/Starr.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 'Starr/DESCRIPTION' ... OK
* this is package 'Starr' 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 'Starr' can be installed ... [30s/32s] 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 ... [87s/89s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot.posBias 27.604 0.366 28.256
plot.gcBias 21.360 0.171 22.005
plot.ma 9.006 0.324 9.683
* 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 'Starr' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ahocorasick.c -o ahocorasick.o
ahocorasick.c:8:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:218:2: note: expanded from macro 'KSEQ_INIT'
KSTREAM_INIT(type_t, __read, 4096) \
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:143:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:119:26: note: expanded from macro '__KS_GETUNTIL'
str->m = str->l + (i - ks->begin) + 1; \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:8:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:218:2: note: expanded from macro 'KSEQ_INIT'
KSTREAM_INIT(type_t, __read, 4096) \
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:143:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:124:25: note: expanded from macro '__KS_GETUNTIL'
str->l = str->l + (i - ks->begin); \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:8:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:218:2: note: expanded from macro 'KSEQ_INIT'
KSTREAM_INIT(type_t, __read, 4096) \
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:143:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:136:15: note: expanded from macro '__KS_GETUNTIL'
return str->l; \
˜˜˜˜˜˜ ˜˜˜˜˜^
ahocorasick.c:8:1: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:221:2: note: expanded from macro 'KSEQ_INIT'
__KSEQ_READ
^˜˜˜˜˜˜˜˜˜˜
./kseq.h:203:58: note: expanded from macro '__KSEQ_READ'
if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:8:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:221:2: note: expanded from macro 'KSEQ_INIT'
__KSEQ_READ
^˜˜˜˜˜˜˜˜˜˜
./kseq.h:195:33: note: expanded from macro '__KSEQ_READ'
if (c != '+') return seq->seq.l; /* FASTA */ \
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^
ahocorasick.c:8:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./kseq.h:221:2: note: expanded from macro 'KSEQ_INIT'
__KSEQ_READ
^˜˜˜˜˜˜˜˜˜˜
./kseq.h:207:19: note: expanded from macro '__KSEQ_READ'
return seq->seq.l; \
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^
ahocorasick.c:233:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
nodep *queue = (nodep *)malloc(sizeof(nodep)*num_nodes);
˜^˜˜˜˜˜˜˜˜
ahocorasick.c:350:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *wlens = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:356:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *nindex = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:362:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *ntext = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:368:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *strand = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:374:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *nmatch = (int*)malloc(INTEGER(wcount_p)[0] * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ahocorasick.c:432:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
pos = getPos(get_complement(seq->seq.s[index]));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ahocorasick.c:493:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
pos = getPos(get_complement(seq->seq.s[index]));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c collect.c -o collect.o
collect.c:23:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ARRAY_RAW((*arr)) = malloc(sizeof(int)*size);
˜^˜˜˜
collect.c:42:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ARRAY_RAW((*arr)) = malloc(sizeof(double)*size);
˜^˜˜˜
collect.c:61:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
double* tmp = malloc(sizeof(double)*(arr->storage_len+size));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
collect.c:76:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int* tmp = malloc(sizeof(int)*(arr->storage_len+size));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rm_small_peak.c -o rm_small_peak.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sort_by_genomic.c -o sort_by_genomic.o
sort_by_genomic.c:59:56: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
t_rec_ptr* recs = malloc(sizeof(t_rec_ptr)*start_arr->len);
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
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 Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Starr.Rcheck/Starr/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 (Starr)