Install eror

[kvshams]

BiocManager::install('HDF5Array')
Bioconductor version 3.9 (BiocManager 1.30.7), R 3.6.1 (2019-07-05)
Installing package(s) 'HDF5Array'
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/HDF5Array_1.12.2.tar.gz'
Content type 'application/x-gzip' length 8045052 bytes (7.7 MB)
==================================================
downloaded 7.7 MB

* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V0XiTa/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DSet.c -o DSet.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V0XiTa/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V0XiTa/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V0XiTa/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c array_selection.c -o array_selection.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V0XiTa/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c h5mread.c -o h5mread.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o HDF5Array.so DSet.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o "/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5.a" "/usr/local/lib/R/site-library/Rhdf5lib/lib/libsz.a" -lz -L/usr/lib/R/lib -lR
gcc: error: "/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5.a": No such file or directory
gcc: error: "/usr/local/lib/R/site-library/Rhdf5lib/lib/libsz.a": No such file or directory
make: *** [/usr/share/R/share/make/shlib.mk:6: HDF5Array.so] Error 1
ERROR: compilation failed for package ‘HDF5Array’
* removing ‘/usr/local/lib/R/site-library/HDF5Array’

The downloaded source packages are in
        ‘/tmp/RtmpCaWCMc/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘HDF5Array’ had non-zero exit status
`

`
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.04

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.7 compiler_3.6.1     tools_3.6.1      

[hpages]

Hi @kvshams,

This is a known issue and is caused by a recent change to Rhdf5lib (in version 1.6.2). It also breaks other packages in Bioconductor 3.9: CoGAPS, DropletUtils, mzR, and ncdfFlow.

The issue is addressed in HDF5Array 1.12.3, which should propagate to the BioC 3.9 repos and become available via BiocManager::install() tomorrow (Oct 16) around 2 pm EST. But you can also get it immediately with:

git clone --branch RELEASE_3_9 https://git.bioconductor.org/packages/HDF5Array
R CMD INSTALL HDF5Array

Hope this helps.

Best, H.

[LTLA]

Missing a CMD, @hpages.

[hpages]

oops, thx @LTLA

[kvshams]

It worked... Awesome!