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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the bcSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bcSeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 133/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bcSeq 1.14.0 (landing page) Jiaxing Lin
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: bcSeq |
Version: 1.14.0 |
Command: rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bcSeq.buildbin-libdir bcSeq_1.14.0.tar.gz |
StartedAt: 2021-10-15 08:09:48 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 08:12:33 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 165.3 seconds |
RetCode: 0 |
Status: OK |
PackageFile: bcSeq_1.14.0.zip |
PackageFileSize: 1.045 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bcSeq.buildbin-libdir bcSeq_1.14.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'bcSeq' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CRISPR_matching.cpp -o CRISPR_matching.o In file included from helper/../structures/Trie.h:16, from helper/count.h:5, from CRISPR_matching.cpp:3: helper/../structures/NodePool.h: In member function 'void Pool::resize()': helper/../structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from helper/../structures/Trie.h:15, from helper/count.h:5, from CRISPR_matching.cpp:3: helper/../structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trie_edit.cpp -o Trie_edit.o In file included from structures/Trie.h:16, from Trie_edit.cpp:1: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from structures/Trie.h:15, from Trie_edit.cpp:1: structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trie_hamming.cpp -o Trie_hamming.o In file included from structures/Trie.h:16, from Trie_hamming.cpp:1: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from structures/Trie.h:15, from Trie_hamming.cpp:1: structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trie_util.cpp -o Trie_util.o In file included from structures/Trie.h:16, from Trie_util.cpp:2: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from structures/Trie.h:15, from Trie_util.cpp:2: structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alignment.cpp -o alignment.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c trimRead.cpp -o trimRead.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uniqueBar.cpp -o uniqueBar.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o bcSeq.dll tmp.def CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -fopenmp -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/bcSeq.buildbin-libdir/00LOCK-bcSeq/00new/bcSeq/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'bcSeq' finding HTML links ... done bcSeq-package html finding level-2 HTML links ... done bcSeq_edit html bcSeq_hamming html trimRead html uniqueBar 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 'bcSeq' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CRISPR_matching.cpp -o CRISPR_matching.o In file included from helper/../structures/Trie.h:16, from helper/count.h:5, from CRISPR_matching.cpp:3: helper/../structures/NodePool.h: In member function 'void Pool::resize()': helper/../structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from helper/../structures/Trie.h:15, from helper/count.h:5, from CRISPR_matching.cpp:3: helper/../structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trie_edit.cpp -o Trie_edit.o In file included from structures/Trie.h:16, from Trie_edit.cpp:1: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from structures/Trie.h:15, from Trie_edit.cpp:1: structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trie_hamming.cpp -o Trie_hamming.o In file included from structures/Trie.h:16, from Trie_hamming.cpp:1: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from structures/Trie.h:15, from Trie_hamming.cpp:1: structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trie_util.cpp -o Trie_util.o In file included from structures/Trie.h:16, from Trie_util.cpp:2: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:52: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(x, buff.get(), count * sizeof(Node)); ^ In file included from structures/Trie.h:15, from Trie_util.cpp:2: structures/Node.h:11:8: note: 'struct Node' declared here struct Node { ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alignment.cpp -o alignment.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c trimRead.cpp -o trimRead.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uniqueBar.cpp -o uniqueBar.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o bcSeq.dll tmp.def CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/bcSeq.buildbin-libdir/bcSeq/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'bcSeq' as bcSeq_1.14.0.zip * DONE (bcSeq)