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Problem installing R package with lblas and lapack dependencies


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0

















I am trying to install the HMSC R package into RStudio Version 1.2.1335 and R version 3.6.1 (2019-07-05) -- "Action of the Toes" on a Linux Ubuntu
18.04.2 LTS System



The code to install through R is as follows



library(devtools)
install_url('https://cran.r-project.org/src/contrib/Archive/BayesLogit/BayesLogit_0.6.tar.gz')
install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))


When installing BayesLogit_0.6.tar.gz I get the following error



/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lblas
/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'BayesLogit.so' failed
make: *** [BayesLogit.so] Error 1
ERROR: compilation failed for package ‘BayesLogit’
* removing ‘/home/barefootbushman/R/x86_64-pc-linux-gnu-library/3.6/BayesLogit’
Error in i.p(...) :
(converted from warning) installation of package ‘/tmp/RtmpL8qXxH/file18aa17542138/BayesLogit_0.6.tar.gz’ had non-zero exit status


I have checked for the installation of -lblas and -lapack using



sudo apt-get update

Hit:1 http://nz.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://nz.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://nz.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 https://repo.skype.com/deb stable InRelease
Hit:5 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease
Get:6 https://desktop-download.mendeley.com/download/apt stable InRelease [2,456 B]
Ign:7 http://dl.bintray.com/basespace/BaseMount-DEB saucy InRelease
Ign:8 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy InRelease
Hit:9 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:10 http://ppa.launchpad.net/inkscape.dev/stable/ubuntu bionic InRelease
Get:11 http://dl.bintray.com/basespace/BaseMount-DEB saucy Release [1,838 B]
Get:12 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy Release [1,837 B]
Hit:13 http://ppa.launchpad.net/marutter/rrutter/ubuntu bionic InRelease
Fetched 6,131 B in 2s (4,067 B/s)
Reading package lists... Done


Followed by



sudo apt-get install libblas-dev liblapack-dev

Reading package lists... Done
Building dependency tree
Reading state information... Done
libblas-dev is already the newest version (3.7.1-4ubuntu1).
liblapack-dev is already the newest version (3.7.1-4ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.


However, I still get the same error when attempting to install BayesLogit in R.



Any help on how to overcome this error would be appreciated.
Chris










share|improve this question





















  • 1





    The installation appear to be picking up a version of gcc from /home/barefootbushman/miniconda3/bin/../lib/gcc in place of the "system" compiler - is this intended?

    – steeldriver
    Aug 6 at 0:11











  • I have miniconda3 installed to run some bioinformatic programs (QIIME2). So unless miniconda3 needs gcc in that directory, no it is not intended.

    – Christopher Kavazos
    Aug 6 at 0:14






  • 1





    In that case I suggest you try setting a more standard PATH in your shell before attempting the installation

    – steeldriver
    Aug 6 at 0:19












  • using .libPaths ?

    – Christopher Kavazos
    Aug 6 at 0:29






  • 1





    ... I was thinking more like . /etc/environment in the terminal before executing R

    – steeldriver
    Aug 6 at 0:33


















0

















I am trying to install the HMSC R package into RStudio Version 1.2.1335 and R version 3.6.1 (2019-07-05) -- "Action of the Toes" on a Linux Ubuntu
18.04.2 LTS System



The code to install through R is as follows



library(devtools)
install_url('https://cran.r-project.org/src/contrib/Archive/BayesLogit/BayesLogit_0.6.tar.gz')
install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))


When installing BayesLogit_0.6.tar.gz I get the following error



/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lblas
/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'BayesLogit.so' failed
make: *** [BayesLogit.so] Error 1
ERROR: compilation failed for package ‘BayesLogit’
* removing ‘/home/barefootbushman/R/x86_64-pc-linux-gnu-library/3.6/BayesLogit’
Error in i.p(...) :
(converted from warning) installation of package ‘/tmp/RtmpL8qXxH/file18aa17542138/BayesLogit_0.6.tar.gz’ had non-zero exit status


I have checked for the installation of -lblas and -lapack using



sudo apt-get update

Hit:1 http://nz.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://nz.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://nz.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 https://repo.skype.com/deb stable InRelease
Hit:5 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease
Get:6 https://desktop-download.mendeley.com/download/apt stable InRelease [2,456 B]
Ign:7 http://dl.bintray.com/basespace/BaseMount-DEB saucy InRelease
Ign:8 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy InRelease
Hit:9 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:10 http://ppa.launchpad.net/inkscape.dev/stable/ubuntu bionic InRelease
Get:11 http://dl.bintray.com/basespace/BaseMount-DEB saucy Release [1,838 B]
Get:12 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy Release [1,837 B]
Hit:13 http://ppa.launchpad.net/marutter/rrutter/ubuntu bionic InRelease
Fetched 6,131 B in 2s (4,067 B/s)
Reading package lists... Done


Followed by



sudo apt-get install libblas-dev liblapack-dev

Reading package lists... Done
Building dependency tree
Reading state information... Done
libblas-dev is already the newest version (3.7.1-4ubuntu1).
liblapack-dev is already the newest version (3.7.1-4ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.


However, I still get the same error when attempting to install BayesLogit in R.



Any help on how to overcome this error would be appreciated.
Chris










share|improve this question





















  • 1





    The installation appear to be picking up a version of gcc from /home/barefootbushman/miniconda3/bin/../lib/gcc in place of the "system" compiler - is this intended?

    – steeldriver
    Aug 6 at 0:11











  • I have miniconda3 installed to run some bioinformatic programs (QIIME2). So unless miniconda3 needs gcc in that directory, no it is not intended.

    – Christopher Kavazos
    Aug 6 at 0:14






  • 1





    In that case I suggest you try setting a more standard PATH in your shell before attempting the installation

    – steeldriver
    Aug 6 at 0:19












  • using .libPaths ?

    – Christopher Kavazos
    Aug 6 at 0:29






  • 1





    ... I was thinking more like . /etc/environment in the terminal before executing R

    – steeldriver
    Aug 6 at 0:33














0












0








0








I am trying to install the HMSC R package into RStudio Version 1.2.1335 and R version 3.6.1 (2019-07-05) -- "Action of the Toes" on a Linux Ubuntu
18.04.2 LTS System



The code to install through R is as follows



library(devtools)
install_url('https://cran.r-project.org/src/contrib/Archive/BayesLogit/BayesLogit_0.6.tar.gz')
install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))


When installing BayesLogit_0.6.tar.gz I get the following error



/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lblas
/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'BayesLogit.so' failed
make: *** [BayesLogit.so] Error 1
ERROR: compilation failed for package ‘BayesLogit’
* removing ‘/home/barefootbushman/R/x86_64-pc-linux-gnu-library/3.6/BayesLogit’
Error in i.p(...) :
(converted from warning) installation of package ‘/tmp/RtmpL8qXxH/file18aa17542138/BayesLogit_0.6.tar.gz’ had non-zero exit status


I have checked for the installation of -lblas and -lapack using



sudo apt-get update

Hit:1 http://nz.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://nz.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://nz.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 https://repo.skype.com/deb stable InRelease
Hit:5 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease
Get:6 https://desktop-download.mendeley.com/download/apt stable InRelease [2,456 B]
Ign:7 http://dl.bintray.com/basespace/BaseMount-DEB saucy InRelease
Ign:8 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy InRelease
Hit:9 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:10 http://ppa.launchpad.net/inkscape.dev/stable/ubuntu bionic InRelease
Get:11 http://dl.bintray.com/basespace/BaseMount-DEB saucy Release [1,838 B]
Get:12 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy Release [1,837 B]
Hit:13 http://ppa.launchpad.net/marutter/rrutter/ubuntu bionic InRelease
Fetched 6,131 B in 2s (4,067 B/s)
Reading package lists... Done


Followed by



sudo apt-get install libblas-dev liblapack-dev

Reading package lists... Done
Building dependency tree
Reading state information... Done
libblas-dev is already the newest version (3.7.1-4ubuntu1).
liblapack-dev is already the newest version (3.7.1-4ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.


However, I still get the same error when attempting to install BayesLogit in R.



Any help on how to overcome this error would be appreciated.
Chris










share|improve this question















I am trying to install the HMSC R package into RStudio Version 1.2.1335 and R version 3.6.1 (2019-07-05) -- "Action of the Toes" on a Linux Ubuntu
18.04.2 LTS System



The code to install through R is as follows



library(devtools)
install_url('https://cran.r-project.org/src/contrib/Archive/BayesLogit/BayesLogit_0.6.tar.gz')
install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))


When installing BayesLogit_0.6.tar.gz I get the following error



/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lblas
/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'BayesLogit.so' failed
make: *** [BayesLogit.so] Error 1
ERROR: compilation failed for package ‘BayesLogit’
* removing ‘/home/barefootbushman/R/x86_64-pc-linux-gnu-library/3.6/BayesLogit’
Error in i.p(...) :
(converted from warning) installation of package ‘/tmp/RtmpL8qXxH/file18aa17542138/BayesLogit_0.6.tar.gz’ had non-zero exit status


I have checked for the installation of -lblas and -lapack using



sudo apt-get update

Hit:1 http://nz.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://nz.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://nz.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 https://repo.skype.com/deb stable InRelease
Hit:5 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease
Get:6 https://desktop-download.mendeley.com/download/apt stable InRelease [2,456 B]
Ign:7 http://dl.bintray.com/basespace/BaseMount-DEB saucy InRelease
Ign:8 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy InRelease
Hit:9 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:10 http://ppa.launchpad.net/inkscape.dev/stable/ubuntu bionic InRelease
Get:11 http://dl.bintray.com/basespace/BaseMount-DEB saucy Release [1,838 B]
Get:12 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy Release [1,837 B]
Hit:13 http://ppa.launchpad.net/marutter/rrutter/ubuntu bionic InRelease
Fetched 6,131 B in 2s (4,067 B/s)
Reading package lists... Done


Followed by



sudo apt-get install libblas-dev liblapack-dev

Reading package lists... Done
Building dependency tree
Reading state information... Done
libblas-dev is already the newest version (3.7.1-4ubuntu1).
liblapack-dev is already the newest version (3.7.1-4ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.


However, I still get the same error when attempting to install BayesLogit in R.



Any help on how to overcome this error would be appreciated.
Chris







18.04 software-installation r source-packages






share|improve this question














share|improve this question











share|improve this question




share|improve this question










asked Aug 6 at 0:01









Christopher KavazosChristopher Kavazos

33 bronze badges




33 bronze badges










  • 1





    The installation appear to be picking up a version of gcc from /home/barefootbushman/miniconda3/bin/../lib/gcc in place of the "system" compiler - is this intended?

    – steeldriver
    Aug 6 at 0:11











  • I have miniconda3 installed to run some bioinformatic programs (QIIME2). So unless miniconda3 needs gcc in that directory, no it is not intended.

    – Christopher Kavazos
    Aug 6 at 0:14






  • 1





    In that case I suggest you try setting a more standard PATH in your shell before attempting the installation

    – steeldriver
    Aug 6 at 0:19












  • using .libPaths ?

    – Christopher Kavazos
    Aug 6 at 0:29






  • 1





    ... I was thinking more like . /etc/environment in the terminal before executing R

    – steeldriver
    Aug 6 at 0:33













  • 1





    The installation appear to be picking up a version of gcc from /home/barefootbushman/miniconda3/bin/../lib/gcc in place of the "system" compiler - is this intended?

    – steeldriver
    Aug 6 at 0:11











  • I have miniconda3 installed to run some bioinformatic programs (QIIME2). So unless miniconda3 needs gcc in that directory, no it is not intended.

    – Christopher Kavazos
    Aug 6 at 0:14






  • 1





    In that case I suggest you try setting a more standard PATH in your shell before attempting the installation

    – steeldriver
    Aug 6 at 0:19












  • using .libPaths ?

    – Christopher Kavazos
    Aug 6 at 0:29






  • 1





    ... I was thinking more like . /etc/environment in the terminal before executing R

    – steeldriver
    Aug 6 at 0:33








1




1





The installation appear to be picking up a version of gcc from /home/barefootbushman/miniconda3/bin/../lib/gcc in place of the "system" compiler - is this intended?

– steeldriver
Aug 6 at 0:11





The installation appear to be picking up a version of gcc from /home/barefootbushman/miniconda3/bin/../lib/gcc in place of the "system" compiler - is this intended?

– steeldriver
Aug 6 at 0:11













I have miniconda3 installed to run some bioinformatic programs (QIIME2). So unless miniconda3 needs gcc in that directory, no it is not intended.

– Christopher Kavazos
Aug 6 at 0:14





I have miniconda3 installed to run some bioinformatic programs (QIIME2). So unless miniconda3 needs gcc in that directory, no it is not intended.

– Christopher Kavazos
Aug 6 at 0:14




1




1





In that case I suggest you try setting a more standard PATH in your shell before attempting the installation

– steeldriver
Aug 6 at 0:19






In that case I suggest you try setting a more standard PATH in your shell before attempting the installation

– steeldriver
Aug 6 at 0:19














using .libPaths ?

– Christopher Kavazos
Aug 6 at 0:29





using .libPaths ?

– Christopher Kavazos
Aug 6 at 0:29




1




1





... I was thinking more like . /etc/environment in the terminal before executing R

– steeldriver
Aug 6 at 0:33






... I was thinking more like . /etc/environment in the terminal before executing R

– steeldriver
Aug 6 at 0:33











1 Answer
1






active

oldest

votes


















0


















To install the HMISC R package in all currently supported versions of Ubuntu open the terminal and type:



sudo apt install r-cran-hmisc 


The r-cran-hmisc package does not depend on either libblas-dev or liblapack-dev, so you won't get a cannot find -lblas or
cannot find -llapack error message when trying to install r-cran-hmisc.



The error message that you got when trying to install the HMISC R package is Anaconda's fault for sure, but I don't know where the culprit Anaconda file is located in your system. Usually when a path is borked by Anaconda you can symbolic link it back to the appropriate Ubuntu executable. If Anaconda has messed up too many paths in your system, the only way you're going to get rid of the mess is by completely uninstalling and purging Anaconda.






share|improve this answer




























  • Thanks Karel, that is what I ultimately did. Completely re-installed Ubuntu. Have not currently got a conda environment but not looking forward to when I need to used QIIME2 again. Hopefully it doesn't mess everything up again!

    – Christopher Kavazos
    Oct 5 at 0:09












Your Answer








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1 Answer
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active

oldest

votes








1 Answer
1






active

oldest

votes









active

oldest

votes






active

oldest

votes









0


















To install the HMISC R package in all currently supported versions of Ubuntu open the terminal and type:



sudo apt install r-cran-hmisc 


The r-cran-hmisc package does not depend on either libblas-dev or liblapack-dev, so you won't get a cannot find -lblas or
cannot find -llapack error message when trying to install r-cran-hmisc.



The error message that you got when trying to install the HMISC R package is Anaconda's fault for sure, but I don't know where the culprit Anaconda file is located in your system. Usually when a path is borked by Anaconda you can symbolic link it back to the appropriate Ubuntu executable. If Anaconda has messed up too many paths in your system, the only way you're going to get rid of the mess is by completely uninstalling and purging Anaconda.






share|improve this answer




























  • Thanks Karel, that is what I ultimately did. Completely re-installed Ubuntu. Have not currently got a conda environment but not looking forward to when I need to used QIIME2 again. Hopefully it doesn't mess everything up again!

    – Christopher Kavazos
    Oct 5 at 0:09















0


















To install the HMISC R package in all currently supported versions of Ubuntu open the terminal and type:



sudo apt install r-cran-hmisc 


The r-cran-hmisc package does not depend on either libblas-dev or liblapack-dev, so you won't get a cannot find -lblas or
cannot find -llapack error message when trying to install r-cran-hmisc.



The error message that you got when trying to install the HMISC R package is Anaconda's fault for sure, but I don't know where the culprit Anaconda file is located in your system. Usually when a path is borked by Anaconda you can symbolic link it back to the appropriate Ubuntu executable. If Anaconda has messed up too many paths in your system, the only way you're going to get rid of the mess is by completely uninstalling and purging Anaconda.






share|improve this answer




























  • Thanks Karel, that is what I ultimately did. Completely re-installed Ubuntu. Have not currently got a conda environment but not looking forward to when I need to used QIIME2 again. Hopefully it doesn't mess everything up again!

    – Christopher Kavazos
    Oct 5 at 0:09













0














0










0









To install the HMISC R package in all currently supported versions of Ubuntu open the terminal and type:



sudo apt install r-cran-hmisc 


The r-cran-hmisc package does not depend on either libblas-dev or liblapack-dev, so you won't get a cannot find -lblas or
cannot find -llapack error message when trying to install r-cran-hmisc.



The error message that you got when trying to install the HMISC R package is Anaconda's fault for sure, but I don't know where the culprit Anaconda file is located in your system. Usually when a path is borked by Anaconda you can symbolic link it back to the appropriate Ubuntu executable. If Anaconda has messed up too many paths in your system, the only way you're going to get rid of the mess is by completely uninstalling and purging Anaconda.






share|improve this answer
















To install the HMISC R package in all currently supported versions of Ubuntu open the terminal and type:



sudo apt install r-cran-hmisc 


The r-cran-hmisc package does not depend on either libblas-dev or liblapack-dev, so you won't get a cannot find -lblas or
cannot find -llapack error message when trying to install r-cran-hmisc.



The error message that you got when trying to install the HMISC R package is Anaconda's fault for sure, but I don't know where the culprit Anaconda file is located in your system. Usually when a path is borked by Anaconda you can symbolic link it back to the appropriate Ubuntu executable. If Anaconda has messed up too many paths in your system, the only way you're going to get rid of the mess is by completely uninstalling and purging Anaconda.







share|improve this answer















share|improve this answer




share|improve this answer








edited Oct 4 at 10:38

























answered Oct 4 at 9:57









karelkarel

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70.1k15 gold badges158 silver badges184 bronze badges















  • Thanks Karel, that is what I ultimately did. Completely re-installed Ubuntu. Have not currently got a conda environment but not looking forward to when I need to used QIIME2 again. Hopefully it doesn't mess everything up again!

    – Christopher Kavazos
    Oct 5 at 0:09

















  • Thanks Karel, that is what I ultimately did. Completely re-installed Ubuntu. Have not currently got a conda environment but not looking forward to when I need to used QIIME2 again. Hopefully it doesn't mess everything up again!

    – Christopher Kavazos
    Oct 5 at 0:09
















Thanks Karel, that is what I ultimately did. Completely re-installed Ubuntu. Have not currently got a conda environment but not looking forward to when I need to used QIIME2 again. Hopefully it doesn't mess everything up again!

– Christopher Kavazos
Oct 5 at 0:09





Thanks Karel, that is what I ultimately did. Completely re-installed Ubuntu. Have not currently got a conda environment but not looking forward to when I need to used QIIME2 again. Hopefully it doesn't mess everything up again!

– Christopher Kavazos
Oct 5 at 0:09


















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