Loading failed during installation

[vagnec]

Hi,

First, I'm aware that h5 is deprecated, but I'm trying to install a package (velocyto.R https://github.com/velocyto-team/velocyto.R ) which has h5 as dependency...

I have this problem while installing h5 : loading fails

install.packages("h5")

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 385k 100 385k 0 0 178k 0 0:00:02 0:00:02 --:--:-- 178k

• installing source package ‘h5’ ...
  ** package ‘h5’ successfully unpacked and MD5 sums checked
  checking for h5c++... /ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/bin/h5c++
  checking for ggrep... /bin/grep
  checking whether /bin/grep accepts -o... yes
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c Attribute.cpp -o Attribute.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c Dataset.cpp -o Dataset.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c Dataspace.cpp -o Dataspace.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c File.cpp -o File.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c Group.cpp -o Group.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c Helpers.cpp -o Helpers.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o
  x86_64-conda_cos6-linux-gnu-cc -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/include -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I"/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c h5_init.c -o h5_init.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -shared -L/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib -L/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib -o h5.so Attribute.o Dataset.o Dataspace.o File.o Group.o Helpers.o RcppExports.o h5_init.o -L/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib -L/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib -L/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib -L. -lhdf5_cpp -lhdf5 -lz -lm -L/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/lib -lR
  installing to /ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/h5/libs
  ** R
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded
  Error: package or namespace load failed for ‘h5’ in dyn.load(file, DLLpath = DLLpath, ...):
  unable to load shared object '/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/h5/libs/h5.so':
  /ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/h5/libs/h5.so: undefined symbol: _ZN2H56H5FileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjRKNS_17FileCreatPropListERKNS_15FileAccPropListE
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing ‘/ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/library/h5’

The downloaded source packages are in
‘/tmp/RtmpxxxxQl/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("h5") :
installation of package ‘h5’ had non-zero exit status

My sessionInfo() is

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux release 6.7 (Carbon)

Matrix products: default
BLAS: /ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/lib/libRblas.so
LAPACK: /ifs/illumina/vagnec/Analyses/software/miniconda/envs/velocyto2/lib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] devtools_1.13.6 RevoUtils_10.0.8 RevoUtilsMath_10.0.1

loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.4.3 R6_2.2.2 tools_3.4.3 withr_2.1.2
[6] curl_3.2 memoise_1.1.0 knitr_1.18 git2r_0.23.0 digest_0.6.15

Thank you in advance for your help

[smanne07]

Hi @vagnec,any luck in installing velocyto by solving the h5 installation problems?