##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:rhdf5filters.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rhdf5filters_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhdf5filters/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5filters’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5filters’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    lib   5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 shell scripts ... 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
* 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 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL rhdf5filters
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘rhdf5filters’ ...
** using staged installation
configuring the BLOSC filter...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether C compiler accepts -msse2... yes
checking for gcc __builtin_cpu_init function... yes
checking for x86 sse2 instruction support... yes
checking whether C compiler accepts -mavx2... yes
checking for x86 avx2 instruction support... yes
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.16.3/Makefile
config.status: creating src/blosc/Makefile
configure:    HDF5_INCLUDE=/src
configure:    BZIP2_LIB=bzip2/libH5Zbz2.so
configure:    BLOSC_LIB=blosc/libH5Zblosc.so
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.16.3/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/Makevars
** libs
make -C blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy.cc
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::Append(const char*, size_t)’:
snappy.cc:1013:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (curr_iov_index_ + 1 >= output_iov_count_) {
             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::AppendFromSelf(size_t, size_t)’:
snappy.cc:1095:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (curr_iov_index_ + 1 >= output_iov_count_) {
               ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: At global scope:
snappy.cc:567:13: warning: ‘void snappy::ComputeTable()’ defined but not used [-Wunused-function]
 static void ComputeTable() {
             ^~~~~~~~~~~~
g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.8.3
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.8.3'
gcc -g -O2 -Wall -fpic -c lz4.c
gcc -g -O2 -Wall -fpic -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.8.3'
make -C lib/zstd-1.3.8
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.3.8'
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.3.8'
make -C lib/blosc-1.16.3 all
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.16.3'
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-avx2.c
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-avx2.c
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-sse2.c
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-sse2.c
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-generic.c
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-generic.c
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c
In file included from shuffle.c:11:0:
shuffle-generic.h:61:13: warning: ‘unshuffle_generic_inline’ defined but not used [-Wunused-function]
 static void unshuffle_generic_inline(const size_t type_size,
             ^~~~~~~~~~~~~~~~~~~~~~~~
shuffle-generic.h:32:13: warning: ‘shuffle_generic_inline’ defined but not used [-Wunused-function]
 static void shuffle_generic_inline(const size_t type_size,
             ^~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c blosclz.c
blosclz.c:219:17: warning: ‘get_match_32’ defined but not used [-Wunused-function]
 static uint8_t *get_match_32(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) {
                 ^~~~~~~~~~~~
blosclz.c:173:17: warning: ‘get_match’ defined but not used [-Wunused-function]
 static uint8_t *get_match(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) {
                 ^~~~~~~~~
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c blosc.c
gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c fastcopy.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.16.3'
rm -f libblosc.a
ar cq libblosc.a lib/blosc-1.16.3/bitshuffle-avx2.o lib/blosc-1.16.3/blosc.o lib/blosc-1.16.3/shuffle-avx2.o lib/blosc-1.16.3/shuffle-sse2.o lib/blosc-1.16.3/bitshuffle-generic.o lib/blosc-1.16.3/blosclz.o lib/blosc-1.16.3/shuffle.o lib/blosc-1.16.3/bitshuffle-sse2.o lib/blosc-1.16.3/fastcopy.o lib/blosc-1.16.3/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.8.3/lz4.o lib/lz4-1.8.3/lz4hc.o lib/zstd-1.3.8/common/debug.o lib/zstd-1.3.8/common/entropy_common.o lib/zstd-1.3.8/common/error_private.o lib/zstd-1.3.8/common/fse_decompress.o lib/zstd-1.3.8/common/pool.o lib/zstd-1.3.8/common/threading.o lib/zstd-1.3.8/common/xxhash.o lib/zstd-1.3.8/common/zstd_common.o lib/zstd-1.3.8/compress/fse_compress.o lib/zstd-1.3.8/compress/hist.o lib/zstd-1.3.8/compress/huf_compress.o lib/zstd-1.3.8/compress/zstd_compress.o lib/zstd-1.3.8/compress/zstd_double_fast.o lib/zstd-1.3.8/compress/zstd_fast.o lib/zstd-1.3.8/compress/zstd_lazy.o lib/zstd-1.3.8/compress/zstd_ldm.o lib/zstd-1.3.8/compress/zstd_opt.o lib/zstd-1.3.8/compress/zstdmt_compress.o lib/zstd-1.3.8/decompress/huf_decompress.o lib/zstd-1.3.8/decompress/zstd_ddict.o lib/zstd-1.3.8/decompress/zstd_decompress.o lib/zstd-1.3.8/decompress/zstd_decompress_block.o
ranlib libblosc.a
gcc  -fpic -c -o H5Zblosc.o H5Zblosc.c \
      -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.16.3
g++ -std=gnu++11 -g -O2 -Wall -fpic -L/usr/local/lib -shared -o libH5Zblosc.so H5Zblosc.o \
	   libblosc.a -lz
make[1]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c bzlib.c
rm -f libbz2.a
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
ranlib libbz2.a
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -Wall -fpic -shared H5Zbzip2.c -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -o libH5Zbz2.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2'
mkdir -p "/home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/
cp blosc/libH5Zblosc.so /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I/usr/local/include  -g -O2 -Wall -fpic  -g -O2  -Wall -c rhdf5filters.c -o rhdf5filters.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rhdf5filters)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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(rhdf5filters)
> 
> test_check("rhdf5filters")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  1.220   0.047   1.252