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###
### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/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’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
42 | Rprintf("What?\n");
| ^~~~~~~
| dprintf
In file included from /usr/include/string.h:495,
from addXS.c:7:
In function ‘strncpy’,
inlined from ‘pastefield’ at addXS.c:17:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:14:19: note: length computed here
14 | int length1 = strlen(text1);
| ^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from addXS.c:7:
In function ‘strncpy’,
inlined from ‘pastefield’ at addXS.c:18:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:15:19: note: length computed here
15 | int length2 = strlen(text2);
| ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c fltbam.c -o fltbam.o
fltbam.c: In function ‘equalkeys’:
fltbam.c:40:21: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness [-Wpointer-sign]
40 | return(strcmp(k1->str, k2->str) == 0);
| ~~^~~~~
| |
| unsigned char *
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:45,
from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
from fltbam.c:2:
/usr/include/string.h:137:32: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
137 | extern int strcmp (const char *__s1, const char *__s2)
| ~~~~~~~~~~~~^~~~
fltbam.c:40:30: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness [-Wpointer-sign]
40 | return(strcmp(k1->str, k2->str) == 0);
| ~~^~~~~
| |
| unsigned char *
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:45,
from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
from fltbam.c:2:
/usr/include/string.h:137:50: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
137 | extern int strcmp (const char *__s1, const char *__s2)
| ~~~~~~~~~~~~^~~~
fltbam.c: In function ‘print_key’:
fltbam.c:45:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
45 | Rprintf("ID: %s, %d\n", k->str, k->length);
| ^~~~~~~
| dprintf
fltbam.c: In function ‘fltbam’:
fltbam.c:91:9: warning: implicit declaration of function ‘Rf_error’; did you mean ‘ferror’? [-Wimplicit-function-declaration]
91 | Rf_error("Fail to open BAM file %s\n", argv[1]);
| ^~~~~~~~
| ferror
fltbam.c:125:25: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness [-Wpointer-sign]
125 | strcpy(k->str, bam1_qname(line));
| ~^~~~~
| |
| unsigned char *
In file included from /usr/include/features.h:461,
from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from fltbam.c:1:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:88:1: note: expected ‘char * restrict’ but argument is of type ‘unsigned char *’
88 | __NTH (strcpy (char *__restrict __dest, const char *__restrict __src))
| ^~~~~
fltbam.c:126:37: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
126 | k->length = strlen(k->str);
| ~^~~~~
| |
| unsigned char *
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:45,
from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
from fltbam.c:2:
/usr/include/string.h:385:35: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
385 | extern size_t strlen (const char *__s)
| ~~~~~~~~~~~~^~~
fltbam.c:96:21: warning: variable ‘kk’ set but not used [-Wunused-but-set-variable]
96 | struct key *k, *kk;
| ^~
In file included from fltbam.c:4:
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
46 | hashtable_iterator_value(struct hashtable_itr *i);
| ^~~~~~~~~~~~~~~~~~~~~~~~
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
32 | hashtable_iterator_key(struct hashtable_itr *i);
| ^~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/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]
29 | 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]
30 | 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]
68 | 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]
69 | 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]
70 | 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]
71 | fgets(line, sizeof(line), infile); // and forth line
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c hashtable_utility.c -o hashtable_utility.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c sam.c -o sam.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o ArrayExpressHTS.so addXS.o bam_plbuf.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o sam.o /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-ArrayExpressHTS/00new/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 from temporary location
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’
Tue Apr 12 03:25:58 2022 [AEHTS] Setting Options Step 1
Tue Apr 12 03:25:58 2022 [AEHTS] Setting Options Step 2
Tue Apr 12 03:25:58 2022 [AEHTS] Setting Options Step 3
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] fasta_formatter not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] cufflinks not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] samtools not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] bwa not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] mmseq not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] bam2hits not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] bowtie not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] tophat not found
Tue Apr 12 03:25:58 2022 [AEHTS]
Tue Apr 12 03:25:58 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Apr 12 03:25:58 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:25:58 2022 [AEHTS]
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
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’
Tue Apr 12 03:26:08 2022 [AEHTS] Setting Options Step 1
Tue Apr 12 03:26:08 2022 [AEHTS] Setting Options Step 2
Tue Apr 12 03:26:08 2022 [AEHTS] Setting Options Step 3
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] fasta_formatter not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] cufflinks not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] samtools not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] bwa not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] mmseq not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] bam2hits not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] bowtie not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] *** WARNING ***
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] tophat not found
Tue Apr 12 03:26:08 2022 [AEHTS]
Tue Apr 12 03:26:08 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Apr 12 03:26:08 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 03:26:08 2022 [AEHTS]
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpressHTS)
