===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir Rbwa_0.99.2.tar.gz'
>>>>>>>
* installing *source* package ‘Rbwa’ ...
** using staged installation
rm -f gmon.out *.o a.out bwa *~ *.a
rm -f bwa
** libs
** arch -
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/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>:85:1: 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>:99:1: note: expanded from here
kh_del_str
^
2 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/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>:34:1: 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>:42:1: 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>:61:1: 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>:77:1: note: expanded from here
kb_del_chn
^
4 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt_gen.c -o bwt_gen.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c rope.c -o rope.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c is.c -o is.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/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/usr/local/include -fPIC -g -Wall -O2 -c bwashm.c -o bwashm.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/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>:18:1: 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>:21:1: 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>:32:1: note: expanded from here
kh_del_b128
^
3 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kopen.c -o kopen.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o
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>:88:1: 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>:99:1: 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>:114:1: 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>:128:1: 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)
^
5 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/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)
===============================
BiocCheckGitClone('Rbwa')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2511/fae455605f915cbb2abfef67f5a471ce84b17a8c/Rbwa.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbwa/DESCRIPTION’ ... OK
* this is package ‘Rbwa’ version ‘0.99.2’
* 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 ... [10s/10s] WARNING
Found the following significant warnings:
rope.c:282:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
rope.c:283:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
rope.c:291:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
rope.c:292:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
rope.c:293:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
rope.c:312:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
rope.c:313:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwashm.c:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
bwashm.c:66:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2511/fae455605f915cbb2abfef67f5a471ce84b17a8c/Rbwa.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2511/fae455605f915cbb2abfef67f5a471ce84b17a8c/Rbwa.Rcheck/00check.log’
for details.
===============================
BiocCheck('Rbwa_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2511/fae455605f915cbb2abfef67f5a471ce84b17a8c/Rbwa_0.99.2.tar.gz" "/tmp/Rtmp7GCD3P/file15126c7000480f/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Rbwa...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters
long.
First 2 lines:
R/utils.R:74 # - All other entries are being collapsed into the form '<...
vignettes/Rbwa.Rmd:118 sequence and the reference genome to be 3 using ...
* NOTE: Consider multiples of 4 spaces for line indents, 65
lines(7%) are not.
First 6 lines:
R/bwa_aln.R:52 program,
R/bwa_aln.R:53 .createFlags(args),
R/bwa_aln.R:54 shQuote(path.expand(index_prefix)),
R/bwa_aln.R:55 fastq_files,
R/bwa_aln.R:56 sai_files)
R/bwa_mem.R:57 program,
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 3
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output