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 1644/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rbwa 1.9.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the Rbwa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbwa.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: Rbwa |
Version: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbwa_1.9.0.tar.gz |
StartedAt: 2024-06-10 08:33:34 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 08:34:18 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 44.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Rbwa.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbwa_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rbwa.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 ‘Rbwa/DESCRIPTION’ ... OK * this is package ‘Rbwa’ version ‘1.9.0’ * 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 ‘Rbwa’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... 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 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 ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rbwa.Rcheck/00check.log’ for details.
Rbwa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbwa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Rbwa’ ... ** using staged installation ** libs gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c utils.c -o utils.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c kthread.c -o kthread.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c kstring.c -o kstring.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c ksw.c -o ksw.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwt.c -o bwt.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bntseq.c -o bntseq.o bntseq.c:40:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, int) ^ ./khash.h:612:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:210:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:84:1: note: expanded from here kh_clear_str ^ bntseq.c:40:1: warning: unused function 'kh_del_str' [-Wunused-function] ./khash.h:612:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:98:1: note: expanded from here kh_del_str ^ 2 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwa.c -o bwa.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwamem.c -o bwamem.o bwamem.c:213:1: warning: unused function 'kb_get_chn' [-Wunused-function] KBTREE_INIT(chn, mem_chain_t, chain_cmp) ^ ./kbtree.h:364:2: note: expanded from macro 'KBTREE_INIT' __KB_GET(name, key_t) \ ^ ./kbtree.h:146:23: note: expanded from macro '__KB_GET' static inline key_t *kb_get_##name(kbtree_##name##_t *b, const key_t k) \ ^ <scratch space>:33:1: note: expanded from here kb_get_chn ^ bwamem.c:213:1: warning: unused function 'kb_interval_chn' [-Wunused-function] ./kbtree.h:365:2: note: expanded from macro 'KBTREE_INIT' __KB_INTERVAL(name, key_t) \ ^ ./kbtree.h:169:21: note: expanded from macro '__KB_INTERVAL' static inline void kb_interval_##name(kbtree_##name##_t *b, const key_t k, key_t **lower, key_t **upper) \ ^ <scratch space>:41:1: note: expanded from here kb_interval_chn ^ bwamem.c:213:1: warning: unused function 'kb_put_chn' [-Wunused-function] ./kbtree.h:366:2: note: expanded from macro 'KBTREE_INIT' __KB_PUT(name, key_t, __cmp) \ ^ ./kbtree.h:225:21: note: expanded from macro '__KB_PUT' static inline void kb_put_##name(kbtree_##name##_t *b, const key_t k) \ ^ <scratch space>:60:1: note: expanded from here kb_put_chn ^ bwamem.c:213:1: warning: unused function 'kb_del_chn' [-Wunused-function] ./kbtree.h:367:2: note: expanded from macro 'KBTREE_INIT' __KB_DEL(name, key_t) ^ ./kbtree.h:326:22: note: expanded from macro '__KB_DEL' static inline key_t kb_del_##name(kbtree_##name##_t *b, const key_t k) \ ^ <scratch space>:76:1: note: expanded from here kb_del_chn ^ 4 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c QSufSort.c -o QSufSort.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwt_gen.c -o bwt_gen.o bwt_gen.c:879:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable] bgint_t oldInverseSa0RelativeRank = 0; ^ bwt_gen.c:953:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable] unsigned int bitsInWordMinusBitPerChar; ^ 2 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c rope.c -o rope.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c rle.c -o rle.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c is.c -o is.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtindex.c -o bwtindex.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwashm.c -o bwashm.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwase.c -o bwase.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtgap.c -o bwtgap.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtaln.c -o bwtaln.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bamlite.c -o bamlite.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwape.c -o bwape.o bwape.c:33:1: warning: unused function 'kh_clear_b128' [-Wunused-function] KHASH_INIT(b128, pair64_t, poslist_t, 1, b128_hash, b128_eq) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:210:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:22:1: note: expanded from here kh_clear_b128 ^ bwape.c:33:1: warning: unused function 'kh_get_b128' [-Wunused-function] ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:217:16: note: expanded from macro '__KHASH_IMPL' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ <scratch space>:25:1: note: expanded from here kh_get_b128 ^ bwape.c:33:1: warning: unused function 'kh_del_b128' [-Wunused-function] ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:36:1: note: expanded from here kh_del_b128 ^ 3 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c kopen.c -o kopen.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c pemerge.c -o pemerge.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c maxk.c -o maxk.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o bwtsw2_core.c:453:45: warning: variable 'n_tot' set but not used [-Wunused-but-set-variable] int i, j, score_mat[16], *heap, heap_size, n_tot = 0; ^ bwtsw2_core.c:23:1: warning: unused function 'kh_get_qintv' [-Wunused-function] KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:217:16: note: expanded from macro '__KHASH_IMPL' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ <scratch space>:87:1: note: expanded from here kh_get_qintv ^ bwtsw2_core.c:23:1: warning: unused function 'kh_del_qintv' [-Wunused-function] ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:98:1: note: expanded from here kh_del_qintv ^ bwtsw2_core.c:24:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, uint64_t) ^ ./khash.h:596:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:210:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ <scratch space>:113:1: note: expanded from here kh_clear_64 ^ bwtsw2_core.c:24:1: warning: unused function 'kh_del_64' [-Wunused-function] ./khash.h:596:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ <scratch space>:127:1: note: expanded from here kh_del_64 ^ bwtsw2_core.c:214:22: warning: unused function 'time_elapse' [-Wunused-function] static inline double time_elapse(const struct rusage *curr, const struct rusage *last) ^ 6 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c fastmap.c -o fastmap.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c main.c -o main.o gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread mkdir -p ../inst cp bwa ../inst/bwa rm -f gmon.out *.o a.out bwa *~ *.a rm -f bwa ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rbwa)
Rbwa.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > library(testthat) > library(Rbwa) > > test_check("Rbwa") [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.05 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.02 sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpqAmjsA/file454c68a4bf5/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fasta/chr12.fa [main] Real time: 0.083 sec; CPU: 0.091 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 7 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c68a4bf5/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fastq/sequences.fastq [main] Real time: 0.048 sec; CPU: 0.052 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c68a4bf5/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads1.fastq [main] Real time: 0.046 sec; CPU: 0.051 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c68a4bf5/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads2.fastq [main] Real time: 0.047 sec; CPU: 0.052 sec [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.05 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.02 sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpqAmjsA/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fasta/chr12.fa [main] Real time: 0.080 sec; CPU: 0.090 sec [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.05 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.02 sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpqAmjsA/file454c596a0735/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fasta/chr12.fa [main] Real time: 0.081 sec; CPU: 0.090 sec [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 7 sequences (133 bp)... [M::mem_process_seqs] Processed 7 reads in 0.001 CPU sec, 0.000 real sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa mem /tmp/RtmpqAmjsA/file454c596a0735/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fastq/sequences.fastq [main] Real time: 0.004 sec; CPU: 0.009 sec [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 8 sequences (808 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 8 reads in 0.001 CPU sec, 0.001 real sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa mem /tmp/RtmpqAmjsA/file454c596a0735/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads1.fastq /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads2.fastq [main] Real time: 0.005 sec; CPU: 0.010 sec [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.05 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.02 sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpqAmjsA/file454c12c139b/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fasta/chr12.fa [main] Real time: 0.083 sec; CPU: 0.094 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 7 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c12c139b/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fastq/sequences.fastq [main] Real time: 0.049 sec; CPU: 0.054 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c12c139b/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads1.fastq [main] Real time: 0.052 sec; CPU: 0.055 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c12c139b/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads2.fastq [main] Real time: 0.047 sec; CPU: 0.052 sec [bwa_aln_core] convert to sequence coordinate... 0.00 sec [bwa_aln_core] refine gapped alignments... 0.00 sec [bwa_aln_core] print alignments... 0.00 sec [bwa_aln_core] 7 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa samse /tmp/RtmpqAmjsA/file454c12c139b/chr12 /tmp/RtmpqAmjsA/file454c12c139b/output.sai /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fastq/sequences.fastq [main] Real time: 0.049 sec; CPU: 0.053 sec [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] fail to infer insert size: too few good pairs [bwa_sai2sam_pe_core] time elapses: 0.00 sec [bwa_sai2sam_pe_core] changing coordinates of 0 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_sai2sam_pe_core] time elapses: 0.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec [bwa_sai2sam_pe_core] print alignments... 0.00 sec [bwa_sai2sam_pe_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa sampe /tmp/RtmpqAmjsA/file454c12c139b/chr12 /tmp/RtmpqAmjsA/file454c12c139b/output1.sai /tmp/RtmpqAmjsA/file454c12c139b/output2.sai /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads1.fastq /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads2.fastq [main] Real time: 0.057 sec; CPU: 0.061 sec [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.05 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.02 sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpqAmjsA/file454c6b4b1c47/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fasta/chr12.fa [main] Real time: 0.081 sec; CPU: 0.091 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 7 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c6b4b1c47/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fastq/sequences.fastq [main] Real time: 0.049 sec; CPU: 0.053 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c6b4b1c47/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads1.fastq [main] Real time: 0.046 sec; CPU: 0.051 sec [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa aln /tmp/RtmpqAmjsA/file454c6b4b1c47/chr12 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads2.fastq [main] Real time: 0.050 sec; CPU: 0.054 sec [bwa_aln_core] convert to sequence coordinate... 0.00 sec [bwa_aln_core] refine gapped alignments... 0.00 sec [bwa_aln_core] print alignments... 0.00 sec [bwa_aln_core] 7 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa samse /tmp/RtmpqAmjsA/file454c6b4b1c47/chr12 /tmp/RtmpqAmjsA/file454c6b4b1c47/output.sai /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/fastq/sequences.fastq [main] Real time: 0.048 sec; CPU: 0.052 sec [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] fail to infer insert size: too few good pairs [bwa_sai2sam_pe_core] time elapses: 0.00 sec [bwa_sai2sam_pe_core] changing coordinates of 0 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_sai2sam_pe_core] time elapses: 0.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec [bwa_sai2sam_pe_core] print alignments... 0.00 sec [bwa_sai2sam_pe_core] 4 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/bwa sampe /tmp/RtmpqAmjsA/file454c6b4b1c47/chr12 /tmp/RtmpqAmjsA/file454c6b4b1c47/output1.sai /tmp/RtmpqAmjsA/file454c6b4b1c47/output2.sai /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads1.fastq /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rbwa/reads/reads2.fastq [main] Real time: 0.055 sec; CPU: 0.060 sec [ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ] > > proc.time() user system elapsed 2.884 1.004 4.206
Rbwa.Rcheck/Rbwa-Ex.timings
name | user | system | elapsed | |
bwa_aln | 0.103 | 0.069 | 0.326 | |
bwa_build_index | 0.076 | 0.022 | 0.106 | |
bwa_mem | 0.086 | 0.036 | 0.134 | |
bwa_sam | 0.132 | 0.107 | 0.259 | |
xa2multi | 0.146 | 0.127 | 0.301 | |