ArrayExpressHTS 1.32.1
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ArrayExpressHTS |
| Branch: RELEASE_3_8 |
| Last Commit: 6c778c1 |
| Last Changed Date: 2019-01-04 13:08:29 -0400 (Fri, 04 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’ [-Wimplicit-function-declaration]
Rprintf("What?\n");
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c fltbam.c -o fltbam.o
In file included from /usr/include/string.h:630:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/samtools/bam.h:47,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/samtools/sam.h:4,
from fltbam.c:2:
fltbam.c: In function ‘equalkeys’:
fltbam.c:40:19: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:19: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:28: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:28: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:19: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:19: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:28: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:28: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:19: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:19: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:19: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:19: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:28: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:28: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:28: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:28: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:19: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:19: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:28: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:28: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:19: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:19: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:28: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^
fltbam.c:40:28: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c: In function ‘print_key’:
fltbam.c:45:5: warning: implicit declaration of function ‘Rprintf’ [-Wimplicit-function-declaration]
Rprintf("ID: %s, %d\n", k->str, k->length);
^
fltbam.c: In function ‘fltbam’:
fltbam.c:91:9: warning: implicit declaration of function ‘Rf_error’ [-Wimplicit-function-declaration]
Rf_error("Fail to open BAM file %s\n", argv[1]);
^
fltbam.c:125:24: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness [-Wpointer-sign]
strcpy(k->str, bam1_qname(line));
^
In file included from /usr/include/features.h:367:0,
from /usr/include/stdio.h:27,
from fltbam.c:1:
/usr/include/x86_64-linux-gnu/bits/string3.h:108:1: note: expected ‘char * restrict’ but argument is of type ‘unsigned char *’
__NTH (strcpy (char *__restrict __dest, const char *__restrict __src))
^
fltbam.c:126:36: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
k->length = strlen(k->str);
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/samtools/bam.h:47:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/samtools/sam.h:4,
from fltbam.c:2:
/usr/include/string.h:394:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
extern size_t strlen (const char *__s)
^
fltbam.c:96:21: warning: variable ‘kk’ set but not used [-Wunused-but-set-variable]
struct key *k, *kk;
^
In file included from fltbam.c:4:0:
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_iterator_value(struct hashtable_itr *i);
^
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_iterator_key(struct hashtable_itr *i);
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c functions.c -o functions.o
functions.c: In function ‘getReadLength’:
functions.c:29:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), infile); // read first line and discard it
^
functions.c:30:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), infile); // read second line and check its length
^
functions.c: In function ‘checkQuality’:
functions.c:68:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), infile); // read first line and discard it
^
functions.c:69:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), infile); // read second line
^
functions.c:70:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), infile); // read third line
^
functions.c:71:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), infile); // and forth line
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c hashtable_utility.c -o hashtable_utility.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/ArrayExpressHTS/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’
No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’
No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’
Mon Apr 15 18:15:57 2019 [AEHTS] Setting Options Step 1
Mon Apr 15 18:15:57 2019 [AEHTS] Setting Options Step 2
Mon Apr 15 18:15:57 2019 [AEHTS] Setting Options Step 3
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] fasta_formatter not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] cufflinks not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] samtools not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] bwa not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] mmseq not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] bam2hits not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] bowtie not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] *** WARNING ***
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] tophat not found
Mon Apr 15 18:15:57 2019 [AEHTS]
Mon Apr 15 18:15:57 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Mon Apr 15 18:15:57 2019 [AEHTS] Use .Rprofile to make options persistent.
Mon Apr 15 18:15:57 2019 [AEHTS]
* DONE (ArrayExpressHTS)