############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ArrayExpressHTS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ArrayExpressHTS’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c addXS.c -o addXS.o addXS.c:42:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] Rprintf("What?\n"); ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fltbam.c -o fltbam.o 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); ^~~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:77:25: note: passing argument to parameter '__s1' here int strcmp(const char *__s1, const char *__s2); ^ 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); ^~~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:77:43: note: passing argument to parameter '__s2' here int strcmp(const char *__s1, const char *__s2); ^ 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:51:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] Rprintf( "\tIndexes for %d mismatches of length %d: ", v->mm, v->length ); ^ fltbam.c:70:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] Rprintf( "Welcome, creating structures...\n" ); ^ 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)); ^~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_string.h:83:27: note: expanded from macro 'strcpy' __builtin___strcpy_chk (dest, __VA_ARGS__, __darwin_obsz (dest)) ^~~~ 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); ^~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:82:28: note: passing argument to parameter '__s' here size_t strlen(const char *__s); ^ fltbam.c:215:9: 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:225:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration] Rf_error("Fail to open BAM file %s\n", argv[2]); ^ In file included from fltbam.c:4: ./hashtable_itr.h:32:1: warning: inline function 'hashtable_iterator_key' is not defined [-Wundefined-inline] hashtable_iterator_key(struct hashtable_itr *i); ^ fltbam.c:189:18: note: used here kk = hashtable_iterator_key(itr); ^ In file included from fltbam.c:4: ./hashtable_itr.h:46:1: warning: inline function 'hashtable_iterator_value' is not defined [-Wundefined-inline] hashtable_iterator_value(struct hashtable_itr *i); ^ fltbam.c:190:17: note: used here v = hashtable_iterator_value(itr); ^ 12 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c functions.c -o functions.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable.c -o hashtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable_itr.c -o hashtable_itr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable_utility.c -o hashtable_utility.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sam.c -o sam.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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 03:41:40 2022 [AEHTS] Setting Options Step 1 Tue Apr 12 03:41:40 2022 [AEHTS] Setting Options Step 2 Tue Apr 12 03:41:40 2022 [AEHTS] Setting Options Step 3 Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] fasta_formatter not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] cufflinks not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] samtools not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] bwa not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] mmseq not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] bam2hits not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] bowtie not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] tophat not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 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 03:41:59 2022 [AEHTS] Setting Options Step 1 Tue Apr 12 03:41:59 2022 [AEHTS] Setting Options Step 2 Tue Apr 12 03:41:59 2022 [AEHTS] Setting Options Step 3 Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] fasta_formatter not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] cufflinks not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] samtools not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] bwa not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] mmseq not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] bam2hits not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] bowtie not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] tophat not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] ** testing if installed package keeps a record of temporary installation path * DONE (ArrayExpressHTS)