Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:35 -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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:bcSeq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings bcSeq_1.14.0.tar.gz |
StartedAt: 2021-10-14 08:57:43 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 08:59:07 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 83.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: bcSeq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:bcSeq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings bcSeq_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/bcSeq.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bcSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bcSeq’ version ‘1.14.0’ * 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 for sufficient/correct file permissions ... 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 ‘/home/biocbuild/bbs-3.13-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 * 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 is not available * 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 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/bcSeq.Rcheck/00check.log’ for details.
bcSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL bcSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘bcSeq’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -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] 58 | 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 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -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] 58 | 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 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -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] 58 | 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 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -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] 58 | 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 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -c alignment.cpp -o alignment.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -c trimRead.cpp -o trimRead.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Matrix/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -c uniqueBar.cpp -o uniqueBar.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o bcSeq.so CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-bcSeq/00new/bcSeq/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 3.865 0.203 4.054
bcSeq.Rcheck/bcSeq-Ex.timings
name | user | system | elapsed | |
bcSeq-package | 0.043 | 0.003 | 0.047 | |
bcSeq_edit | 0.048 | 0.040 | 0.089 | |
bcSeq_hamming | 0.043 | 0.043 | 0.087 | |
trimRead | 0.043 | 0.074 | 0.119 | |
uniqueBar | 0.009 | 0.001 | 0.010 | |