Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-11-26 11:45 -0500 (Tue, 26 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4350 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4108 |
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 1629/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
QuasR 1.47.0 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the QuasR package: - 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 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: QuasR |
Version: 1.47.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QuasR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QuasR_1.47.0.tar.gz |
StartedAt: 2024-11-26 03:25:03 -0500 (Tue, 26 Nov 2024) |
EndedAt: 2024-11-26 03:31:59 -0500 (Tue, 26 Nov 2024) |
EllapsedTime: 416.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: QuasR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QuasR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QuasR_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘QuasR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘QuasR’ version ‘1.47.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘QuasR’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: qQCReport.Rd: ShortReadBase-package Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... INFO 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 ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/QuasR/libs/QuasR.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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 ‘_sprintf’, possibly from ‘sprintf’ (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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed qCount 7.392 0.094 13.444 qMeth 0.215 0.042 6.611 qProject-class 0.199 0.023 5.274 qExportWig 0.051 0.009 5.403 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/00check.log’ for details.
QuasR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL QuasR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘QuasR’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c R_init_QuasR.cpp -o R_init_QuasR.o R_init_QuasR.cpp:2:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:3:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_cat.c -o bam_cat.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cat_bam.c -o cat_bam.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_alignments.c -o count_alignments.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_alignments_subregions.c -o count_alignments_subregions.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c count_junctions.cpp -o count_junctions.o In file included from count_junctions.cpp:1: ./count_junctions.h:2:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:3:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c export_wig.c -o export_wig.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c filter_hisat2.c -o filter_hisat2.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c idxstats_bam.c -o idxstats_bam.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c merge_reorder_sam.cpp -o merge_reorder_sam.o In file included from merge_reorder_sam.cpp:1: ./merge_reorder_sam.h:2:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:3:9: note: previous definition is here #define R_NO_REMAP 1 ^ merge_reorder_sam.cpp:178:16: warning: variable 'nr' set but not used [-Wunused-but-set-variable] static int nr; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o nucleotide_alignment_frequencies.c:59:6: warning: variable 'u' set but not used [-Wunused-but-set-variable] int u = 0; // count of matched position since last mismatch ^ nucleotide_alignment_frequencies.c:62:10: warning: variable 'nm' set but not used [-Wunused-but-set-variable] int32_t nm = 0; // number of mismatch ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profile_alignments.c -o profile_alignments.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c quantify_methylation.cpp -o quantify_methylation.o In file included from quantify_methylation.cpp:5: ./quantify_methylation.h:2:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:3:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o remove_unmapped_from_sam.c:33:12: warning: variable 'count' set but not used [-Wunused-but-set-variable] int r, count = 0; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sam_opts.c -o sam_opts.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sam_utils.c -o sam_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c split_sam_chr.c -o split_sam_chr.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utilities.c -o utilities.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o QuasR.so R_init_QuasR.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_opts.o sam_utils.o split_sam_chr.o utilities.o /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' 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, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches 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 Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat alignment files missing - need to: create alignment index for the genome create 2 genomic alignment(s) Creating an Rbowtie index for /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpdQ8k2y/RtmpdQ8k2y/file13134304e384d.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131345f526001.txt Genomic alignments have been created successfully alignment files missing - need to: create alignment index for the genome create 1 genomic alignment(s) Testing the compute nodes...OK Loading QuasR on the compute nodes...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_13134216f40b4.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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdQ8k2y/file1313470b6334f.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_13134178df524.txt Genomic alignments have been created successfully Creating .fai file for: /Users/biocbuild/bbs-3.21-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-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_13134a098bf6.txt Genomic alignments have been created successfully Creating an Rbowtie index for /Users/biocbuild/bbs-3.21-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...preparing to run on 2 nodes...done Available cores: nodeNames kjohnson3 2 Performing auxiliary alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1313440907bb2.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-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa Creating an Rbowtie index for /Users/biocbuild/bbs-3.21-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-3.21-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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131342942e3fa.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131343cb7f448.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 4 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131343cf94f25.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131347251daab.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-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 4 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131342913274e.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_13134632b8359.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131347af9899e.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 2 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1313416c0cabf.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-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa Finished creating index Testing the compute nodes...OK Loading QuasR on the compute nodes...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131341cba6f7f.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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1313466fe39d.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-3.21-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-3.21-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...preparing to run on 2 nodes...done Available cores: kjohnson3: 2 Performing genomic alignments for 1 samples. See progress in the log file: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_131341f07a8b1.txt Genomic alignments have been created successfully all necessary alignment files found Creating .fai file for: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file131341a93da94.fa all necessary alignment files found Creating .fai file for: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file13134ee8fcc.fa all necessary alignment files found Creating .fai file for: /Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file13134fd04b9b.fa all necessary alignment files found [E::hts_open_format] Failed to open file "no-file" : No such file or directory [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" : No such file or directory [E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/bbs-3.21-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file131347fed4414.sam' [E::hts_open_format] Failed to open file "err" : No such file or directory [E::hts_open_format] Failed to open file "err" : No such file or directory [E::hts_open_format] Failed to open file "err/err" : No such file or directory [E::hts_open_format] Failed to open file "err" : No such file or directory Error in checkForRemoteErrors(lapply(cl, recvResult)) : 2 nodes produced errors; first error: there is no package called ‘does_not_exist’ In addition: Warning messages: 1: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object 2: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object [ FAIL 0 | WARN 0 | SKIP 0 | PASS 409 ] Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (<-localhost:11593) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (<-localhost:11593) > > proc.time() user system elapsed 35.098 2.381 58.384
QuasR.Rcheck/QuasR-Ex.timings
name | user | system | elapsed | |
QuasR-package | 0 | 0 | 0 | |
alignmentStats | 0 | 0 | 0 | |
preprocessReads | 0.544 | 0.006 | 0.551 | |
qAlign | 0 | 0 | 0 | |
qCount | 7.392 | 0.094 | 13.444 | |
qExportWig | 0.051 | 0.009 | 5.403 | |
qMeth | 0.215 | 0.042 | 6.611 | |
qProfile | 0.109 | 0.013 | 0.122 | |
qProject-class | 0.199 | 0.023 | 5.274 | |
qQCReport | 1.199 | 0.018 | 1.218 | |