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This page was generated on 2022-06-24 11:08:26 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for QuasR on lconway


To the developers/maintainers of the QuasR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QuasR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1532/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.37.1  (landing page)
Michael Stadler
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/QuasR
git_branch: master
git_last_commit: ff049af
git_last_commit_date: 2022-05-03 14:20:29 -0400 (Tue, 03 May 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    ERROR    OK  

Summary

Package: QuasR
Version: 1.37.1
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_1.37.1.tar.gz
StartedAt: 2022-06-23 22:01:55 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 22:10:29 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 513.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: QuasR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuasR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuasR’ version ‘1.37.1’
* 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 ... WARNING
Found the following significant warnings:
  count_alignments.c:110:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  count_alignments.c:111:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  export_wig.c:49:49: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  export_wig.c:50:49: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  export_wig.c:62:127: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  export_wig.c:64:99: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  profile_alignments.c:121:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  profile_alignments.c:122:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.ShortReadQQA’ ‘ShortRead:::.qa_adapterContamination’
  ‘ShortRead:::.set_omp_threads’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/QuasR/libs/QuasR.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
qCount         17.351  0.478  34.738
qMeth           0.637  0.173  19.169
qProject-class  0.177  0.103  15.202
qExportWig      0.146  0.032  14.992
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 76412 Segmentation fault: 11  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  23: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  24: test_code(NULL, exprs, env)
  25: source_file(path, child_env(env), wrap = wrap)
  26: FUN(X[[i]], ...)
  27: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  28: doTryCatch(return(expr), name, parentenv, handler)
  29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  30: tryCatchList(expr, classes, parentenv, handlers)
  31: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  32: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
  33: test_files(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package)
  34: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package, parallel = parallel)
  35: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  36: test_check("QuasR")
  An irrecoverable exception occurred. R is aborting now ...
* 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 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/00check.log’
for details.


Installation output

QuasR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL QuasR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘QuasR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_QuasR.cpp -o R_init_QuasR.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_cat.c -o bam_cat.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cat_bam.c -o cat_bam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_alignments.c -o count_alignments.o
count_alignments.c:110:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^
count_alignments.c:110:50: note: use function 'labs' instead
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^~~
                                                 labs
count_alignments.c:111:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^
count_alignments.c:111:50: note: use function 'labs' instead
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^~~
                                                 labs
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_alignments_subregions.c -o count_alignments_subregions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_junctions.cpp -o count_junctions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c export_wig.c -o export_wig.o
export_wig.c:49:49: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
    if((tcov->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < tcov->absIsizeMin) ||
                                                ^
export_wig.c:49:49: note: use function 'labs' instead
    if((tcov->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < tcov->absIsizeMin) ||
                                                ^~~
                                                labs
export_wig.c:50:49: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
       (tcov->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > tcov->absIsizeMax))
                                                ^
export_wig.c:50:49: note: use function 'labs' instead
       (tcov->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > tcov->absIsizeMax))
                                                ^~~
                                                labs
export_wig.c:62:127: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
                    hitPos = (int)((double)bam_calend(&(hit->core), bam1_cigar(hit)) -1 + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                                                     ^
export_wig.c:62:127: note: use function 'labs' instead
                    hitPos = (int)((double)bam_calend(&(hit->core), bam1_cigar(hit)) -1 + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                                                     ^~~
                                                                                                                                     labs
export_wig.c:64:99: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
                hitPos = (int)((double)hit->core.pos + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                  ^
export_wig.c:64:99: note: use function 'labs' instead
                hitPos = (int)((double)hit->core.pos + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                  ^~~
                                                                                                  labs
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter_hisat2.c -o filter_hisat2.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c idxstats_bam.c -o idxstats_bam.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c profile_alignments.c -o profile_alignments.o
profile_alignments.c:121:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^
profile_alignments.c:121:50: note: use function 'labs' instead
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^~~
                                                 labs
profile_alignments.c:122:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^
profile_alignments.c:122:50: note: use function 'labs' instead
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^~~
                                                 labs
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c quantify_methylation.cpp -o quantify_methylation.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_opts.c -o sam_opts.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_utils.c -o sam_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c split_sam_chr.c -o split_sam_chr.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utilities.c -o utilities.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o QuasR.so R_init_QuasR.o bam_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/4.2/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/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)

Tests output

QuasR.Rcheck/tests/testthat.Rout.fail


R version 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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> # 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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rbowtie
> 
> test_check("QuasR")
* installing *source* package ‘BSgenome.HSapiens.QuasR.hg19sub’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
* DONE (BSgenome.HSapiens.QuasR.hg19sub)
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
Creating an Rbowtie index for /private/tmp/RtmpfXExAk/RtmpfXExAk/file12a7cda590fc.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c70d19763.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/RtmpfXExAk/file12a7c3905f0.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c3f0e5eb7.txt
Genomic alignments have been created successfully

Creating .fai file for: /Users/biocbuild/bbs-3.16-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-3.16-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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7cf1ad141.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for /Users/biocbuild/bbs-3.16-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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c5333d5c6.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for /Users/biocbuild/bbs-3.16-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-3.16-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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c7d5cf33d.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c96fde67.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c4635703b.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c39497f38.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-3.16-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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c695e5603.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c53e7a192.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c5edbcf71.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c2e332183.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-3.16-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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c49ab6509.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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c6b43f2ed.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-3.16-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-3.16-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-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12a7c3c145b7.txt
Genomic alignments have been created successfully

all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file12a7c2b78c7b2.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file12a7c1a56b6.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file12a7c72b47e90.fa
all necessary alignment files found

 *** caught segfault ***
address 0x1d092b7b8380, cause 'memory not mapped'

Traceback:
 1: QuasR:::samToSortedBamParallel(file = samf, destination = bout2,     p = 2L, cacheDir = NULL)
 2: eval(code, test_env)
 3: eval(code, test_env)
 4: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
12: test_code(desc, code, env = parent.frame(), reporter = reporter)
13: test_that("samToSortedBamParallel works as expected", {    bamout <- QuasR:::samToSortedBamParallel(file = samf, destination = bout2,         p = 2L, cacheDir = NULL)    expect_identical(bamout, paste0(bout2, ".bam"))    expect_identical(unname(alignmentStats(bamout)), unname(alignmentStats(bamf)))})
14: eval(code, test_env)
15: eval(code, test_env)
16: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
24: test_code(NULL, exprs, env)
25: source_file(path, child_env(env), wrap = wrap)
26: FUN(X[[i]], ...)
27: lapply(test_paths, test_one_file, env = env, wrap = wrap)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
32: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
33: test_files(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package)
34: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package, parallel = parallel)
35: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
36: test_check("QuasR")
An irrecoverable exception occurred. R is aborting now ...

Example timings

QuasR.Rcheck/QuasR-Ex.timings

nameusersystemelapsed
QuasR-package0.0010.0000.001
alignmentStats000
preprocessReads1.5750.0301.611
qAlign000
qCount17.351 0.47834.738
qExportWig 0.146 0.03214.992
qMeth 0.637 0.17319.169
qProfile0.3250.0590.385
qProject-class 0.177 0.10315.202
qQCReport3.3700.1463.551