Cannot install in Google Colab R4.0

Question

Cannot install in Google Colab R4.0

3N4N opened this issue 4 years ago · 3 comments

I'm using Google Colab with python's R magic to run R code. It has BiocManager v3.12. While installing rhdf5filters, it stops without error. I don't have a personal machine with R4.0, so I can't verify if the problem is with Colab or with the installation process.

My command and output are below.

!R -e '.libPaths("/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages");BiocManager::install("rhdf5filters");' > /tmp/Rhdf5filters_install.log

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

  Natural language support but running in an English locale

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.

> .libPaths("/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages");BiocManager::install("rhdf5filters");
configuring the BLOSC filter...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 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
make -C blosc
make[1]: Entering directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -c snappy.cc
g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.8.3
make[2]: Entering directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc/lib/lz4-1.8.3'
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -c lz4.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -c lz4hc.c
make[2]: Leaving directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc/lib/lz4-1.8.3'
make -C lib/zstd-1.3.8
make[2]: Entering directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc/lib/zstd-1.3.8'
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc/lib/zstd-1.3.8'
make -C lib/blosc-1.16.3 all
make[2]: Entering directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc/lib/blosc-1.16.3'
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-avx2.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-avx2.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-sse2.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-sse2.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-generic.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-generic.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/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
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c blosclz.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c blosc.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/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 '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/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 -std=gnu99  -fpic -c -o H5Zblosc.o H5Zblosc.c \
      -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" -I./lib/blosc-1.16.3
g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o libH5Zblosc.so H5Zblosc.o \
	   libblosc.a -lz
make[1]: Leaving directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-wP4Uzq/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -shared H5Zbzip2.c -I"/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -o libH5Zbz2.so
make[1]: Leaving directory '/tmp/RtmplDF1Zr/R.INSTALLcee917252962/rhdf5filters/src/bzip2'
mkdir -p "/content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so /content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/00LOCK-rhdf5filters/00new/rhdf5filters/lib/
Makevars:23: recipe for target 'copying' failed
> 
>

Answer 1 · 2021-05-03T12:13:52.000Z

Thanks for the report. It looks like this is because I was missing quotes around the path where the package is being installed so /content/drive/MyDrive/Colab Notebooks/MultiwayCorrelation/packages/00LOCK-rhdf5filters/00new/rhdf5filters/lib/ gets treated as two paths and the copy fails.

I'd already fixed this in the Bioconductor 3.13 version of the package, but not back-ported it to 3.12. That's now done. You can get a copy immediately from GitHub via:

BiocManager::install('grimbough/rhdf5filters', ref = 'RELEASE_3_12')

It should be available through the standard Bioconductor install method in a few days. Please let me know if this fixes the problem or if it continues to be an issue.

Answer 2 · 2021-05-04T11:52:56.000Z

Installing v3.12 as ref works. Thanks!

Answer 3 · 2021-05-12T09:18:26.000Z

Great, thanks for letting me know.