Angela Goncalves
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ArrayExpressHTS |
| Branch: RELEASE_3_9 |
| Last Commit: 7f2f1e6 |
| Last Changed Date: 2019-06-25 21:04:52 -0400 (Tue, 25 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:48:54 -0400 (Wed, 16 Oct 2019).
| Package 75/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ArrayExpressHTS 1.34.2 Angela Goncalves
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... | ||||||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | [ OK ] | OK | OK | OK | | ||||||
| Package: ArrayExpressHTS |
| Version: 1.34.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpressHTS |
| StartedAt: 2019-10-15 19:04:01 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 19:04:57 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 55.8 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpressHTS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/MacOSX.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/MacOSX.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: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/MacOSX.sdk/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);
^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/string.h:82:28: note: passing argument to parameter '__s' here
size_t strlen(const char *__s);
^
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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c functions.c -o functions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable.c -o hashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable_utility.c -o hashtable_utility.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c sam.c -o sam.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 bam_plbuf.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o sam.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/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 Oct 15 19:04:42 2019 [AEHTS] Setting Options Step 1
Tue Oct 15 19:04:42 2019 [AEHTS] Setting Options Step 2
Tue Oct 15 19:04:42 2019 [AEHTS] Setting Options Step 3
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] fasta_formatter not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] cufflinks not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] samtools not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] bwa not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] mmseq not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] bam2hits not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] bowtie not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] tophat not found
Tue Oct 15 19:04:42 2019 [AEHTS]
Tue Oct 15 19:04:42 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct 15 19:04:42 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:42 2019 [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 Oct 15 19:04:56 2019 [AEHTS] Setting Options Step 1
Tue Oct 15 19:04:56 2019 [AEHTS] Setting Options Step 2
Tue Oct 15 19:04:56 2019 [AEHTS] Setting Options Step 3
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] fasta_formatter not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] cufflinks not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] samtools not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] bwa not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] mmseq not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] bam2hits not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] bowtie not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] *** WARNING ***
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] tophat not found
Tue Oct 15 19:04:56 2019 [AEHTS]
Tue Oct 15 19:04:56 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct 15 19:04:56 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 19:04:56 2019 [AEHTS]
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpressHTS)