Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:59:01 -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: rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scPipe_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scPipe.buildbin-libdir |
StartedAt: 2018-10-17 02:06:54 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 02:08:18 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 83.7 seconds |
RetCode: 0 |
Status: OK |
PackageFile: scPipe_1.2.1.tgz |
PackageFileSize: 1.385 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scPipe_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scPipe.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scPipe.buildbin-libdir scPipe_1.2.1.tar.gz' >>>>>>> * 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 /Users/biocbuild/bbs-3.7-bioc/meat/scPipe.buildbin-libdir/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) >>>>>>> >>>>>>> FIXING LINKS FOR scPipe.buildbin-libdir/scPipe/libs//scPipe.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so" install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so" install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so" install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so"