bcSeq 1.10.0
Jiaxing Lin
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/bcSeq |
| Branch: RELEASE_3_11 |
| Last Commit: 1f1ce58 |
| Last Changed Date: 2020-04-27 15:12:22 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/bcSeq_1.10.0.tar.gz && rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bcSeq.buildbin-libdir bcSeq_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL bcSeq_1.10.0.zip && rm bcSeq_1.10.0.tar.gz bcSeq_1.10.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/bcSeq.buildbin-libdir/bcSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bcSeq' as bcSeq_1.10.0.zip
* DONE (bcSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'bcSeq' successfully unpacked and MD5 sums checked