Package: Rhtslib

Version: 1.15.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhtslib_1.15.5.tar.gz

StartedAt: 2019-04-09 04:59:03 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:59:31 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 28.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rhtslib.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhtslib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhtslib_1.15.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhtslib’ version ‘1.15.5’
* 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:
  src/htslib-1.7/.appveyor.yml
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-3.9-bioc/meat/Rhtslib.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    testdata   4.2Mb
    usrlib     2.3Mb
* 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 ...Error: package or namespace load failed for ‘Rhtslib’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so, 6): Symbol not found: _lzma_easy_buffer_encode
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... WARNING
Error: package or namespace load failed for ‘Rhtslib’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so, 6): Symbol not found: _lzma_easy_buffer_encode
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so, 6): Symbol not found: _lzma_easy_buffer_encode
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
Calls: <Anonymous> ... eval -> eval -> loadNamespace -> library.dynam -> dyn.load
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Error: package or namespace load failed for ‘Rhtslib’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so, 6): Symbol not found: _lzma_easy_buffer_encode
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/libs/Rhtslib.so
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- condi
Execution halted
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/htslib-1.7/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/3.6/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)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_srand48’, possibly from ‘srand48’ (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
* 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: 3 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhtslib
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f "Makefile.Rhtslib"
Makefile.Rhtslib:128: warning: overriding commands for target `.c.o'
/Library/Frameworks/R.framework/Resources/etc/Makeconf:166: warning: ignoring old commands for target `.c.o'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
clang -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
clang -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
clang -g -Wall -O2 -I.  -c -o kstring.o kstring.c
clang -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
clang -g -Wall -O2 -I.  -c -o errmod.o errmod.c
clang -g -Wall -O2 -I.  -c -o faidx.o faidx.c
clang -g -Wall -O2 -I.  -c -o hfile.o hfile.c
clang -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
clang -g -Wall -O2 -I.  -c -o hts.o hts.c
clang -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
clang -g -Wall -O2 -I.  -c -o md5.o md5.c
clang -g -Wall -O2 -I.  -c -o multipart.o multipart.c
clang -g -Wall -O2 -I.  -c -o probaln.o probaln.c
clang -g -Wall -O2 -I.  -c -o realn.o realn.c
clang -g -Wall -O2 -I.  -c -o regidx.o regidx.c
clang -g -Wall -O2 -I.  -c -o sam.o sam.c
clang -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
clang -g -Wall -O2 -I.  -c -o tbx.o tbx.c
clang -g -Wall -O2 -I.  -c -o textutils.o textutils.c
clang -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
clang -g -Wall -O2 -I.  -c -o vcf.o vcf.c
clang -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
clang -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
clang -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
clang -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
clang -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
clang -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
clang -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
clang -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
clang -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
clang -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
clang -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
clang -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
clang -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
clang -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
clang -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.7 -compatibility_version 2  -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o -lz -lm -lbz2 -llzma
ln -sf libhts.dylib libhts.2.dylib
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include"
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib"
cd "htslib-1.7" && cp libhts.a "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib"
clang -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 Rhtslib.so R_init_Rhtslib.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/testdata/tabix"
cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rhtslib/testdata/tabix" 2>/dev/null || true)
installing to /Library/Frameworks/R.framework/Versions/3.6/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)

name	user	system	elapsed
Rhtslib-package	0.028	0.001	0.029
pkgconfig	0.003	0.002	0.006