Luyi Tian
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/scPipe |
| Branch: RELEASE_3_7 |
| Last Commit: 19a1726 |
| Last Changed Date: 2018-05-31 19:42:56 -0400 (Thu, 31 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:59:00 -0400 (Wed, 17 Oct 2018).
| Package 1332/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scPipe 1.2.1 Luyi Tian
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | [ OK ] | OK | WARNINGS | OK | |
| Package: scPipe |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scPipe |
| StartedAt: 2018-10-16 15:53:04 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 15:54:30 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 86.3 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 scPipe
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘scPipe’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Gene.cpp -o Gene.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Interval.cpp -o Interval.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cellbarcode.cpp -o cellbarcode.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c detect_barcode.cpp -o detect_barcode.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c parsebam.cpp -o parsebam.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c parsecount.cpp -o parsecount.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_init' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_BASIC(SCOPE, type_t) \
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:170:16: note: expanded from macro '__KSEQ_BASIC'
SCOPE kseq_t *kseq_init(type_t fd) \
^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_destroy' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_BASIC(SCOPE, type_t) \
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC'
SCOPE void kseq_destroy(kseq_t *ks) \
^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_read' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:242:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_READ(SCOPE)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:190:12: note: expanded from macro '__KSEQ_READ'
SCOPE int kseq_read(kseq_t *seq) \
^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c transcriptmapping.cpp -o transcriptmapping.o
transcriptmapping.cpp:605:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
sam_hdr_write(of, header);
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜
transcriptmapping.cpp:569:10: warning: unused function 'report_every_3_mins' [-Wunused-function]
void report_every_3_mins(atomic<unsigned long long> &cnt, atomic<bool> &running) {
^
In file included from transcriptmapping.cpp:2:
./transcriptmapping.h:138:15: warning: private field 'SOURCE' is not used [-Wunused-private-field]
const int SOURCE = 1;
^
./transcriptmapping.h:142:15: warning: private field 'SCORE' is not used [-Wunused-private-field]
const int SCORE = 5;
^
./transcriptmapping.h:144:15: warning: private field 'PHASE' is not used [-Wunused-private-field]
const int PHASE = 7;
^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp:92:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
sam_hdr_write(fp, hdr);
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -std=gnu++11 -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 scPipe.so Gene.o Interval.o RcppExports.o cellbarcode.o detect_barcode.o parsebam.o parsecount.o rcpp_scPipe_func.o transcriptmapping.o trimbarcode.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/scPipe/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scPipe)