Hervé Pagès
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/Rhtslib |
| git_branch: devel |
| git_last_commit: 31b99ff |
| git_last_commit_date: 2024-04-30 14:38:25 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 1713/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhtslib 3.1.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the Rhtslib package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhtslib.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: Rhtslib |
| Version: 3.1.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rhtslib_3.1.0.tar.gz |
| StartedAt: 2024-06-10 08:52:12 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 08:52:54 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 42.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rhtslib.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rhtslib_3.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rhtslib.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* this is package ‘Rhtslib’ version ‘3.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rhtslib’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rhtslib.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
libs 1.0Mb
testdata 4.8Mb
usrlib 4.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/libs/Rhtslib.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 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.
Rhtslib.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhtslib ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ cd "htslib-1.18" && make -f "Makefile.Rhtslib" echo '/* Default config.h generated by Makefile */' > config.h echo '#ifndef _XOPEN_SOURCE' >> config.h echo '#define _XOPEN_SOURCE 600' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBCURL 1' >> config.h if [ "x" != "x" ] && \ [ "x" != "x" ] && \ [ "x" != "x" ]; then \ echo '#define HAVE_POPCNT 1' >> config.h ; \ echo '#define HAVE_SSE4_1 1' >> config.h ; \ echo '#define HAVE_SSSE3 1' >> config.h ; \ echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> config.h ; \ echo '#define UBSAN 1' >> config.h ; \ echo '#endif' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX2 1' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX512 1' >> config.h ; \ fi clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'clang -arch x86_64' \ '-I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64' \ '-falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden' \ '-L/opt/R/x86_64/lib -fvisibility=hidden' \ '-lz -lm -lbz2 -llzma -lcurl' > config_vars.h clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.o sam_mods.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang -arch x86_64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/x86_64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o ranlib libhts.a clang -arch x86_64 -dynamiclib -install_name /usr/local/lib/libhts.3.dylib -current_version 3.1.18 -compatibility_version 3.1.18 -L/opt/R/x86_64/lib -fvisibility=hidden -o libhts.dylib kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o -lz -lm -lbz2 -llzma -lcurl ln -sf libhts.dylib libhts.3.dylib sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib" cd "htslib-1.18/htslib" && cp * "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib" clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include" -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/usrlib" cd "htslib-1.18" && cp libhts.a "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/usrlib" clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Rhtslib.so R_init_Rhtslib.o /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/testdata/tabix" cd "htslib-1.18/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/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 * DONE (Rhtslib)
Rhtslib.Rcheck/Rhtslib-Ex.timings
| name | user | system | elapsed | |
| Rhtslib-package | 0.025 | 0.004 | 0.032 | |
| pkgconfig | 0.001 | 0.000 | 0.003 | |