Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-11 20:39 -0400 (Fri, 11 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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 |
Package 144/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bcSeq 1.26.0 (landing page) Jiaxing Lin
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the bcSeq package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: bcSeq |
Version: 1.26.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bcSeq.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings bcSeq_1.26.0.tar.gz |
StartedAt: 2024-10-09 22:44:49 -0400 (Wed, 09 Oct 2024) |
EndedAt: 2024-10-09 22:46:51 -0400 (Wed, 09 Oct 2024) |
EllapsedTime: 122.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: bcSeq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bcSeq.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings bcSeq_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/bcSeq.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'bcSeq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'bcSeq' version '1.26.0' * 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:58:16: 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:58:16: 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 'E:/biocbuild/bbs-3.19-bioc/meat/bcSeq.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * 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 x64 is not available File 'E:/biocbuild/bbs-3.19-bioc/R/library/bcSeq/libs/x64/bcSeq.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test_bcSeq.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 2 NOTEs See 'E:/biocbuild/bbs-3.19-bioc/meat/bcSeq.Rcheck/00check.log' for details.
bcSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL bcSeq ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'bcSeq' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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:58:16: 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] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from helper/../structures/Trie.h:15: helper/../structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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:58:16: 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] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from structures/Trie.h:15: structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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:58:16: 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] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from structures/Trie.h:15: structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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:58:16: 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] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from structures/Trie.h:15: structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alignment.cpp -o alignment.o gcc -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c trimRead.cpp -o trimRead.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uniqueBar.cpp -o uniqueBar.o 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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-bcSeq/00new/bcSeq/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (bcSeq)
bcSeq.Rcheck/tests/test_bcSeq.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 4.10 0.32 4.48
bcSeq.Rcheck/bcSeq-Ex.timings
name | user | system | elapsed | |
bcSeq-package | 0.05 | 0.00 | 0.05 | |
bcSeq_edit | 0.13 | 0.02 | 0.14 | |
bcSeq_hamming | 0.11 | 0.00 | 0.11 | |
trimRead | 0.08 | 0.02 | 0.14 | |
uniqueBar | 0.01 | 0.00 | 0.06 | |