| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:35:20 -0400 (Tue, 09 Apr 2019).
| Package 115/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bcSeq 1.5.1 Jiaxing Lin
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: bcSeq |
| Version: 1.5.1 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bcSeq_1.5.1.tar.gz && rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bcSeq.buildbin-libdir bcSeq_1.5.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bcSeq_1.5.1.zip && rm bcSeq_1.5.1.tar.gz bcSeq_1.5.1.zip |
| StartedAt: 2019-04-08 19:15:05 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 19:16:55 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 109.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bcSeq_1.5.1.tar.gz && rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bcSeq.buildbin-libdir bcSeq_1.5.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bcSeq_1.5.1.zip && rm bcSeq_1.5.1.tar.gz bcSeq_1.5.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
100 22788 100 22788 0 0 18331 0 0:00:01 0:00:01 --:--:-- 18436
install for i386
* installing *source* package 'bcSeq' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c CRISPR_matching.cpp -o CRISPR_matching.o
In file included from helper/count.h:5:0,
from CRISPR_matching.cpp:3:
helper/../structures/Trie.h: In member function 'bool state_t::end()':
helper/../structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c Trie_edit.cpp -o Trie_edit.o
In file included from Trie_edit.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c Trie_hamming.cpp -o Trie_hamming.o
In file included from Trie_hamming.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c Trie_util.cpp -o Trie_util.o
In file included from Trie_util.cpp:2:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
Trie_util.cpp: In member function 'bool Trie::setTMat(Rcpp::StringVector, Rcpp::NumericVector)':
Trie_util.cpp:105:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (MatSeq.length() != corLength) {
^
In file included from structures/Trie.h:15:0,
from Trie_util.cpp:2:
structures/Node.h: In member function 'void Trie::addSeq(const string&, int)':
structures/Node.h:31:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i;
^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i;
^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c alignment.cpp -o alignment.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c trimRead.cpp -o trimRead.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c uniqueBar.cpp -o uniqueBar.o
uniqueBar.cpp: In function 'void uniqueBar(Rcpp::String, Rcpp::String)':
uniqueBar.cpp:21:9: warning: unused variable 'length' [-Wunused-variable]
int length = 0;
^
C:/Rtools/mingw_32/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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c CRISPR_matching.cpp -o CRISPR_matching.o
In file included from helper/count.h:5:0,
from CRISPR_matching.cpp:3:
helper/../structures/Trie.h: In member function 'bool state_t::end()':
helper/../structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c Trie_edit.cpp -o Trie_edit.o
In file included from Trie_edit.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c Trie_hamming.cpp -o Trie_hamming.o
In file included from Trie_hamming.cpp:1:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c Trie_util.cpp -o Trie_util.o
In file included from Trie_util.cpp:2:0:
structures/Trie.h: In member function 'bool state_t::end()':
structures/Trie.h:45:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auto end() -> bool { return seqIdx == seq.size() - 1; }
^
Trie_util.cpp: In member function 'bool Trie::setTMat(Rcpp::StringVector, Rcpp::NumericVector)':
Trie_util.cpp:105:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (MatSeq.length() != corLength) {
^
In file included from structures/Trie.h:15:0,
from Trie_util.cpp:2:
structures/Node.h: In member function 'void Trie::addSeq(const string&, int)':
structures/Node.h:31:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i;
^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i;
^
structures/Node.h:53:9: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c alignment.cpp -o alignment.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c trimRead.cpp -o trimRead.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Matrix/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c uniqueBar.cpp -o uniqueBar.o
uniqueBar.cpp: In function 'void uniqueBar(Rcpp::String, Rcpp::String)':
uniqueBar.cpp:21:9: warning: unused variable 'length' [-Wunused-variable]
int length = 0;
^
C:/Rtools/mingw_64/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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/bcSeq.buildbin-libdir/bcSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bcSeq' as bcSeq_1.5.1.zip
* DONE (bcSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'bcSeq' successfully unpacked and MD5 sums checked