velocyto.R installation error : velocyto.R_0.6.tar.gz’ had non-zero exit status

[BeyondMyPast228]

Hi, After Knowing Velocyto, I wanted to install it and do some data analysis. But when I install it, there are always some errors. The error is: /usr/bin/ld: cannot find -lboost_filesystem /usr/bin/ld: cannot find -lboost_system collect2: error: ld returned 1 exit status /usr/share/R/share/make/shlib.mk:6: recipe for target 'velocyto.R.so' failed make: *** [velocyto.R.so] Error 1 ERROR: compilation failed for package ‘velocyto.R’

• removing ‘/home/vip1/R/x86_64-pc-linux-gnu-library/3.6/velocyto.R’ Error: Failed to install 'velocyto.R' from GitHub: (converted from warning) installation of package ‘/tmp/RtmpIlvxHX/file1dde55fac39b1/velocyto.R_0.6.tar.gz’ had non-zero exit status. Can you help me?

[guijie2015]

You need to install boost libraries

[SabrinaITNL]

Hi @guijie2015, I had the same issue and installed the BH package as indicated here https://r-forge.r-project.org/R/?group_id=1469.

However when I try again to install velocyto.R via devtools I get exactly the same error. Do you know I can make R to find the boost libraries?

[BeyondMyPast228]

Hi， What is your operating system? My operating system is Ubuntu. My solution is : RUN apt-get update --yes && apt-get install --no-install-recommends --yes
build-essential
cmake
git
libbamtools-dev
libboost-dev
libboost-iostreams-dev
libboost-log-dev
libboost-system-dev
libboost-test-dev
libssl-dev
libcurl4-openssl-dev
libxml2-dev
libz-dev
curl
libhdf5-cpp-100 \ libarmadillo7
libarmadillo-dev When I manually installed these Lib's one by one, the problem was solved.

[guijie2015]

Hi @guijie2015, I had the same issue and installed the BH package as indicated here https://r-forge.r-project.org/R/?group_id=1469.

However when I try again to install velocyto.R via devtools I get exactly the same error. Do you know I can make R to find the boost libraries?

you need to install boost libraries in your system, not the packages in your R

[eregenyi]

Hi! I had the same issue, thank you for the thread! An additional comment, I was working in a conda environment, installing this from conda forge resolved the issue: https://anaconda.org/conda-forge/boost-cpp

[ishwarvh]

you need to install boost libraries in your system, not the packages in your R

@guijie2015 I have installed the boost libraries as recommended. But I still see the following error related to boost!

/usr/bin/ld: cannot find -lboost_filesystem
/usr/bin/ld: cannot find -lboost_system
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'velocyto.R.so' failed
make: *** [velocyto.R.so] Error 1
ERROR: compilation failed for package ‘velocyto.R’
* removing ‘/home/ishwar/R/x86_64-pc-linux-gnu-library/3.6/velocyto.R’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpVcp7PE/file2dd667f51b8e/velocyto.R_0.6.tar.gz’ had non-zero exit status

Is R not able find the installation path for the boost libraries?

[Junedays]

Same issues

[Marfa-chan]

Same issues in windows