Package: ArrayExpressHTS

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpressHTS

StartedAt: 2018-10-16 16:05:43 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 16:06:21 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 37.8 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpressHTS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/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);
                  ^˜˜˜˜˜˜
/usr/include/string.h:77:25: note: passing argument to parameter here
int      strcmp(const char *, const char *);
                            ^
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);
                           ^˜˜˜˜˜˜
/usr/include/string.h:77:39: note: passing argument to parameter here
int      strcmp(const char *, const char *);
                                          ^
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: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));
                       ^˜˜˜˜˜
/usr/include/secure/_string.h:83:27: note: expanded from macro 'strcpy'
  __builtin___strcpy_chk (dest, src, __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);
                                   ^˜˜˜˜˜
/usr/include/string.h:82:28: note: passing argument to parameter here
size_t   strlen(const char *);
                            ^
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);
                ^
8 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c functions.c -o functions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c hashtable.c -o hashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c hashtable_itr.c -o hashtable_itr.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c hashtable_utility.c -o hashtable_utility.o
clang -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 fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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’
Tue Oct 16 16:06:14 2018 [AEHTS] Setting Options Step 1
Tue Oct 16 16:06:14 2018 [AEHTS] Setting Options Step 2
Tue Oct 16 16:06:14 2018 [AEHTS] Setting Options Step 3
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     fasta_formatter not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     cufflinks not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     samtools not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     bwa not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     mmseq not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     bam2hits not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     bowtie not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING ***
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS]     tophat not found
Tue Oct 16 16:06:14 2018 [AEHTS] 
Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 16 16:06:14 2018 [AEHTS] 
* DONE (ArrayExpressHTS)