Jiaxing Lin
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/bcSeq |
| git_branch: RELEASE_3_14 |
| git_last_commit: 7c51411 |
| git_last_commit_date: 2021-10-26 12:40:11 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:12 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 130/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bcSeq 1.16.0 (landing page) Jiaxing Lin
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bcSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bcSeq_1.16.0.tar.gz |
| StartedAt: 2022-04-12 16:04:09 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:07:05 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 176.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: bcSeq.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bcSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bcSeq_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/bcSeq.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'bcSeq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'bcSeq' version '1.16.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'bcSeq' can be installed ... WARNING Found the following significant warnings: 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] 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] See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/bcSeq.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/bcSeq/libs/i386/bcSeq.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/bcSeq/libs/x64/bcSeq.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test_bcSeq.R' OK ** running tests for arch 'x64' ... Running 'test_bcSeq.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/bcSeq.Rcheck/00check.log' for details.
bcSeq.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/bcSeq_1.16.0.tar.gz && rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bcSeq.buildbin-libdir bcSeq_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL bcSeq_1.16.0.zip && rm bcSeq_1.16.0.tar.gz bcSeq_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 23114 100 23114 0 0 51476 0 --:--:-- --:--:-- --:--:-- 51478
100 23114 100 23114 0 0 51442 0 --:--:-- --:--:-- --:--:-- 51478
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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/bcSeq.buildbin-libdir/bcSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bcSeq' as bcSeq_1.16.0.zip
* DONE (bcSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'bcSeq' successfully unpacked and MD5 sums checked
|
bcSeq.Rcheck/tests_i386/test_bcSeq.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(bcSeq)
> #devtools::load_all("../")
> #### Set the seed
> set.seed(4523)
>
> #### Generate barcode
> lFName <- "./libFile.fasta"
> bases <- c(rep('A', 4), rep('C',4), rep('G',4), rep('T',4))
> numOfBars <- 7
> Barcodes <- rep(NA, numOfBars*2)
> for (i in 1:numOfBars){
+ Barcodes[2*i-1] <- paste0(">barcode_ID: ", i)
+ Barcodes[2*i] <- paste(sample(bases, length(bases)), collapse = '')
+ }
> write(Barcodes, lFName)
>
> #### Generate reads and phred score
> rFName <- "./readFile.fastq"
> numOfReads <- 8
> Reads <- rep(NA, numOfReads*4)
> for (i in 1:numOfReads){
+ Reads[4*i-3] <- paste0("@read_ID_",i)
+ Reads[4*i-2] <- Barcodes[2*sample(1:numOfBars,1,
+ replace=TRUE, prob=seq(1:numOfBars))]
+ Reads[4*i-1] <- "+"
+ Reads[4*i] <- paste(rawToChar(as.raw(
+ 33+sample(20:30, length(bases),replace=TRUE))),
+ collapse='')
+ }
> write(Reads, rFName)
>
> #### perform alignment
> ReadFile <- "./readFile.fastq"
> BarFile <- "./libFile.fasta"
> outFile <- "./countH.csv"
>
> #### with default output for bcSeq_hamming
> #res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = TRUE )
> #res <- read.csv(outFile, header=FALSE)
> #res
>
> #### with return of alignment probability matrix to R
> #outFile <- "./countH2.csv"
> #res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = FALSE )
> #res
>
> #### with default output for bcSeq_edit
> outFile <- "./countE.csv"
> #res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = TRUE,
> # gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> # pen_max = 7)
> #res <- read.csv(outFile, header=FALSE)
> #res
>
> #### with return of alignment probability matrix to R
> #outFile <- "./countE2.csv"
> #res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = FALSE,
> # gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> # pen_max = 7)
> #res
>
> #### user-defined probability model
> comstomizeP <- function(m, x, y)
+ {
+ x * (1 - log(2) + log(1 + m / (m + y) ) )
+ }
> outFile = "comstomizeP.csv"
> #bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = TRUE,
> # gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> # pen_max = 7, userProb = comstomizeP)
>
> proc.time()
user system elapsed
4.01 0.29 5.06
|
bcSeq.Rcheck/tests_x64/test_bcSeq.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(bcSeq)
> #devtools::load_all("../")
> #### Set the seed
> set.seed(4523)
>
> #### Generate barcode
> lFName <- "./libFile.fasta"
> bases <- c(rep('A', 4), rep('C',4), rep('G',4), rep('T',4))
> numOfBars <- 7
> Barcodes <- rep(NA, numOfBars*2)
> for (i in 1:numOfBars){
+ Barcodes[2*i-1] <- paste0(">barcode_ID: ", i)
+ Barcodes[2*i] <- paste(sample(bases, length(bases)), collapse = '')
+ }
> write(Barcodes, lFName)
>
> #### Generate reads and phred score
> rFName <- "./readFile.fastq"
> numOfReads <- 8
> Reads <- rep(NA, numOfReads*4)
> for (i in 1:numOfReads){
+ Reads[4*i-3] <- paste0("@read_ID_",i)
+ Reads[4*i-2] <- Barcodes[2*sample(1:numOfBars,1,
+ replace=TRUE, prob=seq(1:numOfBars))]
+ Reads[4*i-1] <- "+"
+ Reads[4*i] <- paste(rawToChar(as.raw(
+ 33+sample(20:30, length(bases),replace=TRUE))),
+ collapse='')
+ }
> write(Reads, rFName)
>
> #### perform alignment
> ReadFile <- "./readFile.fastq"
> BarFile <- "./libFile.fasta"
> outFile <- "./countH.csv"
>
> #### with default output for bcSeq_hamming
> #res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = TRUE )
> #res <- read.csv(outFile, header=FALSE)
> #res
>
> #### with return of alignment probability matrix to R
> #outFile <- "./countH2.csv"
> #res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = FALSE )
> #res
>
> #### with default output for bcSeq_edit
> outFile <- "./countE.csv"
> #res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = TRUE,
> # gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> # pen_max = 7)
> #res <- read.csv(outFile, header=FALSE)
> #res
>
> #### with return of alignment probability matrix to R
> #outFile <- "./countE2.csv"
> #res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = FALSE,
> # gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> # pen_max = 7)
> #res
>
> #### user-defined probability model
> comstomizeP <- function(m, x, y)
+ {
+ x * (1 - log(2) + log(1 + m / (m + y) ) )
+ }
> outFile = "comstomizeP.csv"
> #bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> # tMat = NULL, numThread = 2, count_only = TRUE,
> # gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> # pen_max = 7, userProb = comstomizeP)
>
> proc.time()
user system elapsed
4.12 0.15 4.26
|
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bcSeq.Rcheck/examples_i386/bcSeq-Ex.timings
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bcSeq.Rcheck/examples_x64/bcSeq-Ex.timings
|