Michael Stadler
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/QuasR |
| git_branch: RELEASE_3_18 |
| git_last_commit: 04c8406 |
| git_last_commit_date: 2023-11-01 08:10:31 -0400 (Wed, 01 Nov 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:09 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1639/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| QuasR 1.42.1 (landing page) Michael Stadler
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.42.1 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings QuasR_1.42.1.tar.gz |
| StartedAt: 2024-03-28 04:07:08 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:19:46 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 757.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: QuasR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings QuasR_1.42.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* 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 '1.42.1'
* 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 ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking installed package size ... NOTE
installed size is 12.0Mb
sub-directories of 1Mb or more:
extdata 1.0Mb
libs 10.2Mb
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-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 22.28 0.49 45.79
qMeth 0.42 0.20 21.78
qProject-class 0.20 0.06 18.56
qExportWig 0.21 0.03 18.41
* 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
'F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/00check.log'
for details.
QuasR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL QuasR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'QuasR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.3.0' using C++ compiler: 'G__~1.EXE (GCC) 12.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c quantify_methylation.cpp -o quantify_methylation.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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-3.18-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: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, setdiff, sort, 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-3.18-bioc/tmpdir/RtmpWAfBZk/RtmpWAfBZk\file114e84ee4754c.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e87622e26.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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e84dfc1d27.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-3.18-bioc\tmpdir\RtmpWAfBZk\file114e86fea7ec2.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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e8202165e1.txt
Genomic alignments have been created successfully
Creating .fai file for: F:/biocbuild/bbs-3.18-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-3.18-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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e821b7164b.txt
Genomic alignments have been created successfully
Creating an Rbowtie index for F:/biocbuild/bbs-3.18-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
PALOMINO4
2
Performing auxiliary alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e84cf42a9.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-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: F:/biocbuild/bbs-3.18-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-3.18-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-3.18-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-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for F:/biocbuild/bbs-3.18-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-3.18-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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e87ebaa34.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e8592b6c72.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:
PALOMINO4: 2
Performing genomic alignments for 4 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e871d978b0.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e8a6aa08.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-3.18-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:
PALOMINO4: 2
Performing genomic alignments for 4 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e8485f2b8f.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e8571136a9.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e831aa5d5f.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e819011bc.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-3.18-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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e81ef879af.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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e822814fc9.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-3.18-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-3.18-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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_114e8edd7902.txt
Genomic alignments have been created successfully
all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file114e823841e6e.fa
all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file114e81f373ec8.fa
all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file114e86fc12bd7.fa
all necessary alignment files found
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection
[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-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file114e86e657af7.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
52.15 5.06 200.42
QuasR.Rcheck/QuasR-Ex.timings
| name | user | system | elapsed | |
| QuasR-package | 0 | 0 | 0 | |
| alignmentStats | 0 | 0 | 0 | |
| preprocessReads | 1.77 | 0.01 | 1.81 | |
| qAlign | 0 | 0 | 0 | |
| qCount | 22.28 | 0.49 | 45.79 | |
| qExportWig | 0.21 | 0.03 | 18.41 | |
| qMeth | 0.42 | 0.20 | 21.78 | |
| qProfile | 0.43 | 0.14 | 0.60 | |
| qProject-class | 0.20 | 0.06 | 18.56 | |
| qQCReport | 4.33 | 0.11 | 4.55 | |