Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:48 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the QuasR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QuasR.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 1484/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
QuasR 1.32.0 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: QuasR |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QuasR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QuasR_1.32.0.tar.gz |
StartedAt: 2021-10-14 22:47:13 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:58:37 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 684.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: QuasR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QuasR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QuasR_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘QuasR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘QuasR’ version ‘1.32.0’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘QuasR’ can be installed ... OK * 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 ... NOTE Unexported objects imported by ':::' calls: ‘ShortRead:::.ShortReadQQA’ ‘ShortRead:::.qa_adapterContamination’ ‘ShortRead:::.set_omp_threads’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call(ShortRead:::.set_omp_threads, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE GNU make is a SystemRequirements. * 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 File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/QuasR/libs/QuasR.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘_srand48’, possibly from ‘srand48’ (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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed qCount 21.752 0.579 45.629 qMeth 1.082 0.263 26.694 qProject-class 0.232 0.118 18.499 qExportWig 0.146 0.038 20.403 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/00check.log’ for details.
QuasR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL QuasR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘QuasR’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_QuasR.cpp -o R_init_QuasR.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam.c -o bam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_cat.c -o bam_cat.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cat_bam.c -o cat_bam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c count_alignments.c -o count_alignments.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c count_alignments_subregions.c -o count_alignments_subregions.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c count_junctions.cpp -o count_junctions.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c export_wig.c -o export_wig.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c filter_hisat2.c -o filter_hisat2.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c idxstats_bam.c -o idxstats_bam.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c profile_alignments.c -o profile_alignments.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c quantify_methylation.cpp -o quantify_methylation.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sam.c -o sam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sam_utils.c -o sam_utils.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c split_sam_chr.c -o split_sam_chr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utilities.c -o utilities.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o QuasR.so R_init_QuasR.o bam.o bam_cat.o bam_plbuf.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o filter_hisat2.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o sam.o sam_utils.o split_sam_chr.o utilities.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-QuasR/00new/QuasR/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 (QuasR)
QuasR.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > > library(testthat) > library(QuasR) Loading required package: parallel Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Rbowtie > > test_check("QuasR") * installing *source* package ‘BSgenome.HSapiens.QuasR.hg19sub’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices * DONE (BSgenome.HSapiens.QuasR.hg19sub) Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit alignment files missing - need to: create alignment index for the genome create 2 genomic alignment(s) Creating an Rbowtie index for /private/tmp/RtmpPKIKe5/RtmpPKIKe5/file10ef511545548.fa Finished creating index * installing *source* package ‘BSgenome.HSapiens.QuasR.hg19sub.Rbowtie’ ... ** using staged installation ** inst ** help *** installing help indices ** building package indices ** 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 (BSgenome.HSapiens.QuasR.hg19sub.Rbowtie) Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef537aaf2db.txt Genomic alignments have been created successfully alignment files missing - need to: create alignment index for the genome create 1 genomic alignment(s) Creating an RbowtieCtoT index for /tmp/RtmpPKIKe5/file10ef511cd4eff.fa Finished creating index * installing *source* package ‘BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT’ ... ** using staged installation ** inst ** help *** installing help indices ** building package indices ** 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 (BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT) Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef52dd7d0f7.txt Genomic alignments have been created successfully Creating .fai file for: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa alignment files missing - need to: create alignment index for the genome create 2 genomic alignment(s) create 2 auxiliary alignment(s) Creating an Rbowtie index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef56cdd7ebe.txt Genomic alignments have been created successfully Creating an Rbowtie index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/NC_001422.1.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: nodeNames machv2.bioconductor.org 2 Performing auxiliary alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef544fc6dca.txt Auxiliary alignments have been created successfully alignment files missing - need to: create alignment index for the genome create 2 genomic alignment(s) Reading and processing the SNP file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa Creating a .fai file for the snp genome: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Creating a .fai file for the snp genome: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa Creating an Rbowtie index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Finished creating index Creating an Rbowtie index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef54b160c70.txt Genomic alignments have been created successfully alignment files missing - need to: create 2 genomic alignment(s) Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef57738e9bc.txt Genomic alignments have been created successfully alignment files missing - need to: create 4 genomic alignment(s) Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 4 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef527f356da.txt Genomic alignments have been created successfully alignment files missing - need to: create 2 genomic alignment(s) Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef569b3261f.txt Genomic alignments have been created successfully alignment files missing - need to: create alignment index for the genome create 4 genomic alignment(s) Creating an Rhisat2 index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 4 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef5be158e6.txt Genomic alignments have been created successfully alignment files missing - need to: create 2 genomic alignment(s) Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef529b0781e.txt Genomic alignments have been created successfully alignment files missing - need to: create splice site file for gene annotation create 2 genomic alignment(s) Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef51e12125c.txt Genomic alignments have been created successfully alignment files missing - need to: create splice site file for gene annotation create 2 genomic alignment(s) Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef56aa4acbf.txt Genomic alignments have been created successfully alignment files missing - need to: create alignment index for the genome create 1 genomic alignment(s) Creating an RbowtieCtoT index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef513955701.txt Genomic alignments have been created successfully alignment files missing - need to: create 1 genomic alignment(s) Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef5108e870e.txt Genomic alignments have been created successfully alignment files missing - need to: create alignment index for the genome create 1 genomic alignment(s) Creating an RbowtieCtoT index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Finished creating index Creating an RbowtieCtoT index for /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: machv2.bioconductor.org: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_10ef57f391e2f.txt Genomic alignments have been created successfully all necessary alignment files found Creating .fai file for: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file10ef57d48e973.fa all necessary alignment files found Creating .fai file for: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file10ef51fe2f878.fa all necessary alignment files found Creating .fai file for: /Users/biocbuild/bbs-3.13-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file10ef52ab3a93e.fa all necessary alignment files found [E::hts_open_format] Failed to open file no-file [samopen] no @SQ lines in the header. samtools cat: fail to open output file 'not-there/bfile': No such file or directory [E::hts_open_format] Failed to open file err [E::hts_open_format] Failed to open file err [E::hts_open_format] Failed to open file err [E::hts_open_format] Failed to open file err/err [E::hts_open_format] Failed to open file err [ FAIL 0 | WARN 0 | SKIP 0 | PASS 398 ] > > proc.time() user system elapsed 130.232 9.559 209.948
QuasR.Rcheck/QuasR-Ex.timings
name | user | system | elapsed | |
QuasR-package | 0.000 | 0.000 | 0.001 | |
alignmentStats | 0 | 0 | 0 | |
preprocessReads | 1.769 | 0.042 | 1.814 | |
qAlign | 0.000 | 0.000 | 0.001 | |
qCount | 21.752 | 0.579 | 45.629 | |
qExportWig | 0.146 | 0.038 | 20.403 | |
qMeth | 1.082 | 0.263 | 26.694 | |
qProfile | 0.692 | 0.100 | 0.793 | |
qProject-class | 0.232 | 0.118 | 18.499 | |
qQCReport | 4.311 | 0.124 | 4.442 | |