ArrayExpressHTS 1.10.0
Angela Goncalves , Andrew Tikhonov
| 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/ArrayExpressHTS | | 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 | N O T S U P P O R T E D |
| 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/ArrayExpressHTS.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 'ArrayExpressHTS/DESCRIPTION' ... OK
* this is package 'ArrayExpressHTS' 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 'ArrayExpressHTS' can be installed ... [37s/39s] 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
cleanupCluster: no visible global function definition for
'cleanupClusters'
prepareCluster: no visible global function definition for
'mergeClusters'
* 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 ... [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
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck/00check.log'
for details.
* installing *source* package 'ArrayExpressHTS' ...
** 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 -ggdb -O0 -Wall -pedantic -Wconversion -c addXS.c -o addXS.o
addXS.c:14:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int length1 = strlen(text1);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
addXS.c:15:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int length2 = strlen(text2);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
addXS.c:42:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
Rprintf("What?\n");
^
3 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 -ggdb -O0 -Wall -pedantic -Wconversion -c fltbam.c -o fltbam.o
In file included from fltbam.c:2:
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);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
fltbam.c:30:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
hash = ((hash << 5) + hash) + c; /* hash * 33 + c */
˜ ^
fltbam.c:40:19: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^˜˜˜˜˜˜
/usr/include/string.h:92:25: note: passing argument to parameter here
int strcmp(const char *, const char *);
^
fltbam.c:40:28: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^˜˜˜˜˜˜
/usr/include/string.h:92:39: note: passing argument to parameter here
int strcmp(const char *, const char *);
^
fltbam.c:45:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
Rprintf("ID: %s, %d\n", k->str, k->length);
^
fltbam.c:91:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration]
Rf_error("Fail to open BAM file %s\n", argv[1]);
^
fltbam.c:125:24: warning: passing 'unsigned char [50]' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
strcpy(k->str, bam1_qname(line));
^˜˜˜˜˜
/usr/include/secure/_string.h:85:30: note: expanded from macro 'strcpy'
? __builtin___strcpy_chk (dest, src, __darwin_obsz (dest)) \
^
fltbam.c:125:24: warning: passing 'unsigned char [50]' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
strcpy(k->str, bam1_qname(line));
^˜˜˜˜˜
/usr/include/secure/_string.h:86:27: note: expanded from macro 'strcpy'
: __inline_strcpy_chk (dest, src))
^
/usr/include/secure/_string.h:89:39: note: passing argument to parameter '__dest' here
__inline_strcpy_chk (char *__restrict __dest, const char *__restrict __src)
^
fltbam.c:126:36: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k->length = strlen(k->str);
^˜˜˜˜˜
/usr/include/string.h:98:28: note: passing argument to parameter here
size_t strlen(const char *);
^
fltbam.c:136:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
found->index[0] = i-1;
˜ ˜^˜
fltbam.c:147:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
found->index[0] = i-1;
˜ ˜^˜
fltbam.c:155:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
found->index[found->length] = i-1;
˜ ˜^˜
fltbam.c:181:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *allind = malloc(tindex * sizeof (int));
^˜˜˜˜˜ ˜
fltbam.c:192:31: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
allind[i+j] = v->index[j];
˜ ^˜˜˜˜˜˜˜˜˜˜
fltbam.c:201:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort (allind, tindex, sizeof(int), int_cmp);
˜˜˜˜˜ ^˜˜˜˜˜
fltbam.c:126:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
k->length = strlen(k->str);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
17 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 -ggdb -O0 -Wall -pedantic -Wconversion -c functions.c -o functions.o
functions.c:132:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int strlength = strlen(p_seq);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
functions.c:195:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int strlength = strlen(p_qual);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
functions.c:272:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int strlength = strlen(p_seq);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
3 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 -ggdb -O0 -Wall -pedantic -Wconversion -c hashtable.c -o hashtable.o
hashtable.c:23:31: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
const float max_load_factor = 0.65;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
1 warning 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 -ggdb -O0 -Wall -pedantic -Wconversion -c hashtable_itr.c -o hashtable_itr.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 -ggdb -O0 -Wall -pedantic -Wconversion -c hashtable_utility.c -o hashtable_utility.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 ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Wed May 1 02:24:36 2013 [AEHTS] Setting Options Step 1
Wed May 1 02:24:36 2013 [AEHTS] Setting Options Step 2
Wed May 1 02:24:36 2013 [AEHTS] Setting Options Step 3
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] fasta_formatter not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] cufflinks not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] samtools not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] bwa not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] mmseq not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] bam2hits not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] bowtie not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] *** WARNING ***
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] tophat not found
Wed May 1 02:24:36 2013 [AEHTS]
Wed May 1 02:24:36 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Wed May 1 02:24:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed May 1 02:24:36 2013 [AEHTS]
* DONE (ArrayExpressHTS)