Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1642/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
QuasR 1.46.0 (landing page) Michael Stadler
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.46.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings QuasR_1.46.0.tar.gz |
StartedAt: 2024-12-20 04:56:38 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:11:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 894.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: QuasR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings QuasR_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'QuasR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'QuasR' version '1.46.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'QuasR' can be installed ... WARNING Found the following significant warnings: quantify_methylation.cpp:1077:57: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] quantify_methylation.cpp:1077:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wformat=] quantify_methylation.cpp:1077:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=] See 'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.3.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking installed package size ... NOTE installed size is 13.2Mb sub-directories of 1Mb or more: extdata 1.0Mb libs 11.3Mb * 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 ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/QuasR/libs/x64/QuasR.dll': Found '_assert', possibly from 'assert' (C) 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed qCount 25.50 0.60 57.54 qQCReport 4.70 0.08 6.00 qMeth 0.47 0.20 28.05 qExportWig 0.19 0.03 20.25 qProject-class 0.11 0.11 20.27 * 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, 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/00check.log' for details.
QuasR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL QuasR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'QuasR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_QuasR.cpp -o R_init_QuasR.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam_cat.c -o bam_cat.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cat_bam.c -o cat_bam.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count_alignments.c -o count_alignments.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count_alignments_subregions.c -o count_alignments_subregions.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count_junctions.cpp -o count_junctions.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c export_wig.c -o export_wig.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extract_unmapped_reads.c -o extract_unmapped_reads.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c filter_hisat2.c -o filter_hisat2.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c idxstats_bam.c -o idxstats_bam.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c merge_reorder_sam.cpp -o merge_reorder_sam.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c profile_alignments.c -o profile_alignments.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c quantify_methylation.cpp -o quantify_methylation.o quantify_methylation.cpp: In function 'SEXPREC* quantify_methylation_singleAlignments(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': quantify_methylation.cpp:1077:57: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 1077 | Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n", | ~~^ | | | long int | %lld 1078 | resLength, data.Cid.size(), data.meth.size()); | ~~~~~~~~~ | | | R_xlen_t {aka long long int} quantify_methylation.cpp:1077:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wformat=] 1077 | Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n", | ~~^ | | | long unsigned int | %llu 1078 | resLength, data.Cid.size(), data.meth.size()); | ~~~~~~~~~~~~~~~ | | | std::vector<unsigned int>::size_type {aka long long unsigned int} quantify_methylation.cpp:1077:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=] 1077 | Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n", | ~~^ | | | long unsigned int | %llu 1078 | resLength, data.Cid.size(), data.meth.size()); | ~~~~~~~~~~~~~~~~ | | | std::vector<int>::size_type {aka long long unsigned int} gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sam_opts.c -o sam_opts.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sam_utils.c -o sam_utils.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c split_sam_chr.c -o split_sam_chr.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utilities.c -o utilities.o g++ -std=gnu++17 -shared -s -static-libgcc -o QuasR.dll tmp.def 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 F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-QuasR/00new/QuasR/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 (QuasR)
QuasR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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. > # 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: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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpwvdRvF/RtmpwvdRvF\filea810166d6b17.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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81076c61069.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: palomino8: 2 Performing genomic alignments for 1 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81041877222.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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpwvdRvF\filea8106e5173c0.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: palomino8: 2 Performing genomic alignments for 1 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a8106ee33d39.txt Genomic alignments have been created successfully Creating .fai file for: F:/biocbuild/bbs-3.20-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 F:/biocbuild/bbs-3.20-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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81066a212bb.txt Genomic alignments have been created successfully Creating an Rbowtie index for F:/biocbuild/bbs-3.20-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 palomino8 2 Performing auxiliary alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a8105aca6ca8.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: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt Creating the genome fasta file containing the SNPs: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Creating the genome fasta file containing the SNPs: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa Creating a .fai file for the snp genome: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Creating a .fai file for the snp genome: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa Creating an Rbowtie index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Finished creating index Creating an Rbowtie index for F:/biocbuild/bbs-3.20-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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81029c4232d.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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81050ca38db.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: palomino8: 2 Performing genomic alignments for 4 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a8105749708c.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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81038cc4b0.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 F:/biocbuild/bbs-3.20-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: palomino8: 2 Performing genomic alignments for 4 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a810da11e3d.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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81079335c99.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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81031524f20.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: palomino8: 2 Performing genomic alignments for 2 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81041d71e1d.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 F:/biocbuild/bbs-3.20-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: palomino8: 2 Performing genomic alignments for 1 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a8106a615115.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: palomino8: 2 Performing genomic alignments for 1 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a81017a6235f.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 F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa Finished creating index Creating an RbowtieCtoT index for F:/biocbuild/bbs-3.20-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: palomino8: 2 Performing genomic alignments for 1 samples. See progress in the log file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_a8102a2f2049.txt Genomic alignments have been created successfully all necessary alignment files found Creating .fai file for: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/filea81079da2094.fa all necessary alignment files found Creating .fai file for: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/filea810794270a.fa all necessary alignment files found Creating .fai file for: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/filea81048117ad5.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 'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/filea8106e1e668f.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' [ FAIL 0 | WARN 0 | SKIP 0 | PASS 409 ] > > proc.time() user system elapsed 61.35 6.68 282.67
QuasR.Rcheck/QuasR-Ex.timings
name | user | system | elapsed | |
QuasR-package | 0 | 0 | 0 | |
alignmentStats | 0 | 0 | 0 | |
preprocessReads | 1.85 | 0.01 | 2.02 | |
qAlign | 0 | 0 | 0 | |
qCount | 25.50 | 0.60 | 57.54 | |
qExportWig | 0.19 | 0.03 | 20.25 | |
qMeth | 0.47 | 0.20 | 28.05 | |
qProfile | 0.45 | 0.08 | 0.98 | |
qProject-class | 0.11 | 0.11 | 20.27 | |
qQCReport | 4.70 | 0.08 | 6.00 | |