##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ArrayExpressHTS.buildbin-libdir && mkdir ArrayExpressHTS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ArrayExpressHTS_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ArrayExpressHTS.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ArrayExpressHTS.buildbin-libdir ArrayExpressHTS_1.38.0.tar.gz'
>>>>>>> 

* 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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/ArrayExpressHTS.buildbin-libdir/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’
Sat Oct 17 06:36:59 2020 [AEHTS] Setting Options Step 1
Sat Oct 17 06:36:59 2020 [AEHTS] Setting Options Step 2
Sat Oct 17 06:36:59 2020 [AEHTS] Setting Options Step 3
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     fasta_formatter not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     cufflinks not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     samtools not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     bwa not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     mmseq not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     bam2hits not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     bowtie not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS]     tophat not found
Sat Oct 17 06:36:59 2020 [AEHTS] 
Sat Oct 17 06:36:59 2020 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Sat Oct 17 06:36:59 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:36:59 2020 [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’
Sat Oct 17 06:37:14 2020 [AEHTS] Setting Options Step 1
Sat Oct 17 06:37:14 2020 [AEHTS] Setting Options Step 2
Sat Oct 17 06:37:14 2020 [AEHTS] Setting Options Step 3
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     fasta_formatter not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     cufflinks not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     samtools not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     bwa not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     mmseq not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     bam2hits not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     bowtie not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] *** WARNING ***
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS]     tophat not found
Sat Oct 17 06:37:14 2020 [AEHTS] 
Sat Oct 17 06:37:14 2020 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Sat Oct 17 06:37:14 2020 [AEHTS] Use .Rprofile to make options persistent.
Sat Oct 17 06:37:14 2020 [AEHTS] 
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpressHTS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ArrayExpressHTS.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ArrayExpressHTS.so"