############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ArrayExpressHTS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘ArrayExpressHTS’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/Rhtslib/include/bam.h:45, from /home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/Rhtslib/include/bam.h:45, from /home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/Rhtslib/include/bam.h:45, from /home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-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’ Thu Oct 14 06:15:42 2021 [AEHTS] Setting Options Step 1 Thu Oct 14 06:15:42 2021 [AEHTS] Setting Options Step 2 Thu Oct 14 06:15:42 2021 [AEHTS] Setting Options Step 3 Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] fasta_formatter not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] cufflinks not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] samtools not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] bwa not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] mmseq not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] bam2hits not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] bowtie not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] tophat not found Thu Oct 14 06:15:42 2021 [AEHTS] Thu Oct 14 06:15:42 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Thu Oct 14 06:15:42 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:42 2021 [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’ Thu Oct 14 06:15:54 2021 [AEHTS] Setting Options Step 1 Thu Oct 14 06:15:54 2021 [AEHTS] Setting Options Step 2 Thu Oct 14 06:15:54 2021 [AEHTS] Setting Options Step 3 Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] fasta_formatter not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] cufflinks not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] samtools not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] bwa not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] mmseq not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] bam2hits not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] bowtie not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] *** WARNING *** Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] tophat not found Thu Oct 14 06:15:54 2021 [AEHTS] Thu Oct 14 06:15:54 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Thu Oct 14 06:15:54 2021 [AEHTS] Use .Rprofile to make options persistent. Thu Oct 14 06:15:54 2021 [AEHTS] ** testing if installed package keeps a record of temporary installation path * DONE (ArrayExpressHTS)