############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/qrqc_1.48.0.tar.gz && rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qrqc.buildbin-libdir qrqc_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL qrqc_1.48.0.zip && rm qrqc_1.48.0.tar.gz qrqc_1.48.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 347k 1 5189 0 0 7414 0 0:00:48 --:--:-- 0:00:48 7412 100 347k 100 347k 0 0 375k 0 --:--:-- --:--:-- --:--:-- 375k install for i386 * installing *source* package 'qrqc' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_io.c -o R_init_io.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o In file included from io.c:12: C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: 'kseq_destroy' defined but not used [-Wunused-function] SCOPE void kseq_destroy(kseq_t *ks) \ ^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC' __KSEQ_BASIC(SCOPE, type_t) \ ^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^~~~~~~~~~ io.c:29:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(FILE_TYPE*, gzreadclone) ^~~~~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/qrqc.buildbin-libdir/00LOCK-qrqc/00new/qrqc/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'qrqc' finding HTML links ... done FASTASummary-class html FASTQSummary-class html SequenceSummary-class html basePlot-methods html calcKL html gcPlot-methods html geom_qlinerange html getBase-methods html getBaseProp-methods html getGC-methods html getKmer-methods html getMCQual-methods html getQual-methods html getSeqlen-methods html kmerEntropyPlot html kmerKLPlot html list2df html makeReport html plotBases html plotGC html plotQuals html plotSeqLengths html qualPlot-methods html readSeqFile html scale_color_dna html scale_color_iupac html seqlenPlot-methods html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'qrqc' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_io.c -o R_init_io.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o In file included from io.c:12: C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: 'kseq_destroy' defined but not used [-Wunused-function] SCOPE void kseq_destroy(kseq_t *ks) \ ^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC' __KSEQ_BASIC(SCOPE, type_t) \ ^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^~~~~~~~~~ io.c:29:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(FILE_TYPE*, gzreadclone) ^~~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'qrqc' as qrqc_1.48.0.zip * DONE (qrqc) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'qrqc' successfully unpacked and MD5 sums checked