Michael Stadler
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 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 -0500 (Wed, 01 Nov 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:43 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 | | ||||||||
| lconway | 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: /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_1.42.1.tar.gz |
| StartedAt: 2024-03-03 22:46:37 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 22:58:05 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 688.0 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_1.42.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuasR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuasR’ version ‘1.42.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘QuasR’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 21.533 0.788 45.385
qMeth 0.711 0.197 22.104
qProject-class 0.194 0.103 18.566
qExportWig 0.150 0.032 18.748
* 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/Resources/library’ * installing *source* package ‘QuasR’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_QuasR.cpp -o R_init_QuasR.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_cat.c -o bam_cat.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cat_bam.c -o cat_bam.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_alignments.c -o count_alignments.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_alignments_subregions.c -o count_alignments_subregions.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_junctions.cpp -o count_junctions.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c export_wig.c -o export_wig.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c filter_hisat2.c -o filter_hisat2.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c idxstats_bam.c -o idxstats_bam.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profile_alignments.c -o profile_alignments.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c quantify_methylation.cpp -o quantify_methylation.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sam_opts.c -o sam_opts.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sam_utils.c -o sam_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c split_sam_chr.c -o split_sam_chr.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utilities.c -o utilities.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/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/4.3-x86_64/Resources/library/00LOCK-QuasR/00new/QuasR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (QuasR)
QuasR.Rcheck/tests/testthat.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
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/tmp/RtmpJ5MQ2c/RtmpJ5MQ2c/file11cb0a4828c7.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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb076d2617.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:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb03603a758.txt
Genomic alignments have been created successfully
alignment files missing - need to:
create alignment index for the genome
create 1 genomic alignment(s)
Creating an RbowtieCtoT index for /tmp/RtmpJ5MQ2c/file11cb06403944.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:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb0673f5dd9.txt
Genomic alignments have been created successfully
Creating .fai file for: /Users/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 /Users/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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb01c93518b.txt
Genomic alignments have been created successfully
Creating an Rbowtie index for /Users/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
lconway
2
Performing auxiliary alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb0339e0130.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-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: /Users/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: /Users/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: /Users/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: /Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for /Users/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 /Users/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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb03ec5e77e.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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb039cd36f2.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:
lconway: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb05b12b948.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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb013205181.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-3.18-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:
lconway: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb02ee5ab45.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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb050e7e675.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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb02796bade.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:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb05f079823.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-3.18-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:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb02f1d6968.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:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb02fb1e3e2.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-3.18-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-3.18-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:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_11cb02c280b8b.txt
Genomic alignments have been created successfully
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file11cb01c0a8278.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file11cb01043eab6.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file11cb076c21483.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-3.18-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file11cb05b7441c2.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 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (<-localhost:11482)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (<-localhost:11482)
>
> proc.time()
user system elapsed
123.077 11.684 205.404
QuasR.Rcheck/QuasR-Ex.timings
| name | user | system | elapsed | |
| QuasR-package | 0.000 | 0.001 | 0.001 | |
| alignmentStats | 0.000 | 0.001 | 0.002 | |
| preprocessReads | 1.794 | 0.053 | 1.874 | |
| qAlign | 0.000 | 0.001 | 0.000 | |
| qCount | 21.533 | 0.788 | 45.385 | |
| qExportWig | 0.150 | 0.032 | 18.748 | |
| qMeth | 0.711 | 0.197 | 22.104 | |
| qProfile | 0.406 | 0.072 | 0.483 | |
| qProject-class | 0.194 | 0.103 | 18.566 | |
| qQCReport | 4.102 | 0.135 | 4.269 | |