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girke-lab / ChemmineOB

OpenBabel wrapper package for R
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Failed to install ChemmineOB package #23

Closed QizhiSu closed 2 years ago

QizhiSu commented 4 years ago

Dear all, I am now working with ubuntu 18.04.4. I have installed the openbable 3.0.0 by using snap install. However, I failed to install the chemmineOB 1.25.1 package. please see the attachment below: 79691669-43411a00-8261-11ea-8a9b-688eb98266dc 79691678-4cca8200-8261-11ea-8049-88c1cd4714ee 79691682-548a2680-8261-11ea-8c02-50a2c29a9f01 it seems that openbabel was not detected when installing ChemmineOB package. I have tried to compile openbabel myself, but i fail to do that. i am quite nerd in compiling. Please help.

khoran commented 4 years ago

Sorry for the late reply. If you're still trying to get this to work, could you send me the full compile command you used to build ChemmineOB? Your third picture only shows the error part. Thanks.

yonicd commented 3 years ago

getting the same error on ubuntu 18.04 R 4.0.2

12/22 15:19:32.278 (GMT)
Installing ChemmineOB (1.28.0) ...
12/22 15:19:32.368 (GMT)
curl: HTTP 200 https://bioconductor.org/packages/3.12/data/annotation/src/contrib/PACKAGES.rds
12/22 15:19:32.435 (GMT)
curl: HTTP 200 https://bioconductor.org/packages/3.12/data/experiment/src/contrib/PACKAGES.rds
12/22 15:19:32.513 (GMT)
curl: HTTP 200 https://bioconductor.org/packages/3.12/bioc/src/contrib/PACKAGES.rds
12/22 15:19:32.607 (GMT)
curl: HTTP 200 https://bioconductor.org/packages/3.12/workflows/src/contrib/PACKAGES.rds
12/22 15:19:32.698 (GMT)
curl: HTTP 200 https://cran.rstudio.com/src/contrib/PACKAGES.rds
12/22 15:19:34.197 (GMT)
curl: HTTP 200 https://bioconductor.org/packages/3.12/bioc/src/contrib/ChemmineOB_1.28.0.tar.gz
12/22 15:19:35.599 (GMT)
[1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/opt/R/4.0.2/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/RtmpUCeIWS/packrat-install-52c6be0fc92/ChemmineOB' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package ‘ChemmineOB’ ...\n** using staged installation\nchecking for pkg-config... /usr/bin/pkg-config\nchecking pkg-config is at least version 0.9.0... yes\nchecking for OPENBABEL... no\nchecking for OPENBABEL... no\nchecking for gcc... gcc\nchecking whether the C compiler works... yes\nchecking for C compiler default output file name... a.out\nchecking for suffix of executables... \nchecking whether we are cross compiling... no\nchecking for suffix of object files... o\nchecking whether we are using the GNU C compiler... yes\nchecking whether gcc accepts -g... yes\nchecking for gcc option
to accept ISO C89... none needed\nchecking how to run the C preprocessor... gcc -E\nconfigure: creating ./config.status\nconfig.status: creating src/Makevars\n** libs\ng++ -std=gnu++11 -I\"/opt/R/4.0.2/lib/R/include\" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/Cellar/eigen/3.3.8_1/include/eigen3 -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3 -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/BH/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o\nChemmineOB.cpp:1569:10: fatal error: openbabel/obutil.h: No such file or directory\n #include <openbabel/obutil.h>\n ^~~~~~~~~~~~~~~~~~~~\ncompilation terminated.\n/opt/R/4.0.2/lib/R/etc/Makeconf:176: recipe for target 'ChemmineOB.o' failed\nmake: *** [ChemmineOB.o] Error 1\nERROR: compilation failed for package ‘ChemmineOB’\n* removing ‘/opt/rstudio-conn
ect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/ChemmineOB’"
12/22 15:19:35.603 (GMT)
Error: Command failed (1)
12/22 15:19:35.603 (GMT)
12/22 15:19:35.603 (GMT)
Failed to run system command:
12/22 15:19:35.603 (GMT)
12/22 15:19:35.603 (GMT)
'/opt/R/4.0.2/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/RtmpUCeIWS/packrat-install-52c6be0fc92/ChemmineOB' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2' --install-tests --no-docs --no-multiarch --no-demo
12/22 15:19:35.603 (GMT)
12/22 15:19:35.603 (GMT)
The command failed with output:
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* installing *source* package ‘ChemmineOB’ ...
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** using staged installation
12/22 15:19:35.603 (GMT)
checking for pkg-config... /usr/bin/pkg-config
12/22 15:19:35.603 (GMT)
checking pkg-config is at least version 0.9.0... yes
12/22 15:19:35.603 (GMT)
checking for OPENBABEL... no
12/22 15:19:35.603 (GMT)
checking for OPENBABEL... no
12/22 15:19:35.603 (GMT)
checking for gcc... gcc
12/22 15:19:35.603 (GMT)
checking whether the C compiler works... yes
12/22 15:19:35.603 (GMT)
checking for C compiler default output file name... a.out
12/22 15:19:35.603 (GMT)
checking for suffix of executables...
12/22 15:19:35.603 (GMT)
checking whether we are cross compiling... no
12/22 15:19:35.603 (GMT)
checking for suffix of object files... o
12/22 15:19:35.603 (GMT)
checking whether we are using the GNU C compiler... yes
12/22 15:19:35.603 (GMT)
checking whether gcc accepts -g... yes
12/22 15:19:35.603 (GMT)
checking for gcc option to accept ISO C89... none needed
12/22 15:19:35.603 (GMT)
checking how to run the C preprocessor... gcc -E
12/22 15:19:35.603 (GMT)
configure: creating ./config.status
12/22 15:19:35.603 (GMT)
config.status: creating src/Makevars
12/22 15:19:35.603 (GMT)
** libs
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g++ -std=gnu++11 -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/Cellar/eigen/3.3.8_1/include/eigen3 -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3 -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/BH/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o
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ChemmineOB.cpp:1569:10: fatal error: openbabel/obutil.h: No such file or directory
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#include <openbabel/obutil.h>
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^~~~~~~~~~~~~~~~~~~~
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compilation terminated.
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/opt/R/4.0.2/lib/R/etc/Makeconf:176: recipe for target 'ChemmineOB.o' failed
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make: *** [ChemmineOB.o] Error 1
12/22 15:19:35.603 (GMT)
ERROR: compilation failed for package ‘ChemmineOB’
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* removing ‘/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/ChemmineOB’
12/22 15:19:35.603 (GMT)
12/22 15:19:35.603 (GMT)
Unable to fully restore the R packages associated with this deployment.
12/22 15:19:35.603 (GMT)
Please review the preceding messages to determine which package
12/22 15:19:35.603 (GMT)
encountered installation difficulty and the cause of the failure.
Build error: exit status 1
tgirke commented 3 years ago

Make sure you install it via

BiocManager::install("ChemmineOB")

Also, the latest Bioc version you want to install first is 3.12 that uses R-4.0.3. In addition, for OpenBabel you need version >=3.x.x since ChemmineOB was just upgraded to using the newer one.

Thomas

On Tue, Dec 22, 2020 at 7:23 AM yonicd notifications@github.com wrote:

getting the same error on ubuntu 18.04 R 4.0

12/22 15:19:32.278 (GMT)

Installing ChemmineOB (1.28.0) ...

12/22 15:19:32.368 (GMT)

curl: HTTP 200 https://bioconductor.org/packages/3.12/data/annotation/src/contrib/PACKAGES.rds

12/22 15:19:32.435 (GMT)

curl: HTTP 200 https://bioconductor.org/packages/3.12/data/experiment/src/contrib/PACKAGES.rds

12/22 15:19:32.513 (GMT)

curl: HTTP 200 https://bioconductor.org/packages/3.12/bioc/src/contrib/PACKAGES.rds

12/22 15:19:32.607 (GMT)

curl: HTTP 200 https://bioconductor.org/packages/3.12/workflows/src/contrib/PACKAGES.rds

12/22 15:19:32.698 (GMT)

curl: HTTP 200 https://cran.rstudio.com/src/contrib/PACKAGES.rds

12/22 15:19:34.197 (GMT)

curl: HTTP 200 https://bioconductor.org/packages/3.12/bioc/src/contrib/ChemmineOB_1.28.0.tar.gz

12/22 15:19:35.599 (GMT)

[1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/opt/R/4.0.2/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/RtmpUCeIWS/packrat-install-52c6be0fc92/ChemmineOB' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n installing source* package ‘ChemmineOB’ ...\n** using staged installation\nchecking for pkg-config... /usr/bin/pkg-config\nchecking pkg-config is at least version 0.9.0... yes\nchecking for OPENBABEL... no\nchecking for OPENBABEL... no\nchecking for gcc... gcc\nchecking whether the C compiler works... yes\nchecking for C compiler default output file name... a.out\nchecking for suffix of executables... \nchecking whether we are cross compiling... no\nchecking for suffix of object files... o\nchecking whether we are using the GNU C compiler... yes\nchecking whether gcc accepts -g... yes\nchecking for gcc option

to accept ISO C89... none needed\nchecking how to run the C preprocessor... gcc -E\nconfigure: creating ./config.status\nconfig.status: creating src/Makevars\n** libs\ng++ -std=gnu++11 -I\"/opt/R/4.0.2/lib/R/include\" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/Cellar/eigen/3.3.8_1/include/eigen3 -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3 -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/BH/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o\nChemmineOB.cpp:1569:10: fatal error: openbabel/obutil.h: No such file or directory\n #include <openbabel/obutil.h>\n ^~~~~~~~\ncompilation terminated.\n/opt/R/4.0.2/lib/R/etc/Makeconf:176: recipe for target 'ChemmineOB.o' failed\nmake: ** [ChemmineOB.o] Error 1\nERROR: compilation failed for package ‘ChemmineOB’\n removing ‘/opt/rstudio-conn

ect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/ChemmineOB’"

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Error: Command failed (1)

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12/22 15:19:35.603 (GMT)

Failed to run system command:

12/22 15:19:35.603 (GMT)

12/22 15:19:35.603 (GMT)

'/opt/R/4.0.2/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/RtmpUCeIWS/packrat-install-52c6be0fc92/ChemmineOB' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2' --install-tests --no-docs --no-multiarch --no-demo

12/22 15:19:35.603 (GMT)

12/22 15:19:35.603 (GMT)

The command failed with output:

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  • installing source package ‘ChemmineOB’ ...

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** using staged installation

12/22 15:19:35.603 (GMT)

checking for pkg-config... /usr/bin/pkg-config

12/22 15:19:35.603 (GMT)

checking pkg-config is at least version 0.9.0... yes

12/22 15:19:35.603 (GMT)

checking for OPENBABEL... no

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checking for OPENBABEL... no

12/22 15:19:35.603 (GMT)

checking for gcc... gcc

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checking whether the C compiler works... yes

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checking for C compiler default output file name... a.out

12/22 15:19:35.603 (GMT)

checking for suffix of executables...

12/22 15:19:35.603 (GMT)

checking whether we are cross compiling... no

12/22 15:19:35.603 (GMT)

checking for suffix of object files... o

12/22 15:19:35.603 (GMT)

checking whether we are using the GNU C compiler... yes

12/22 15:19:35.603 (GMT)

checking whether gcc accepts -g... yes

12/22 15:19:35.603 (GMT)

checking for gcc option to accept ISO C89... none needed

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checking how to run the C preprocessor... gcc -E

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configure: creating ./config.status

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config.status: creating src/Makevars

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** libs

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g++ -std=gnu++11 -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/Cellar/eigen/3.3.8_1/include/eigen3 -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3 -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/BH/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o

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ChemmineOB.cpp:1569:10: fatal error: openbabel/obutil.h: No such file or directory

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include <openbabel/obutil.h>

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^~~~~~~~

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compilation terminated.

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/opt/R/4.0.2/lib/R/etc/Makeconf:176: recipe for target 'ChemmineOB.o' failed

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make: *** [ChemmineOB.o] Error 1

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ERROR: compilation failed for package ‘ChemmineOB’

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  • removing ‘/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.2/ChemmineOB’

12/22 15:19:35.603 (GMT)

12/22 15:19:35.603 (GMT)

Unable to fully restore the R packages associated with this deployment.

12/22 15:19:35.603 (GMT)

Please review the preceding messages to determine which package

12/22 15:19:35.603 (GMT)

encountered installation difficulty and the cause of the failure.

Build error: exit status 1

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/girke-lab/ChemmineOB/issues/23#issuecomment-749595628, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKGMVH6DEGN4B6LFJ33NNLSWC2VPANCNFSM4MNGT6VA .

-- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521

E-mail: thomas.girke@ucr.edu URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437

yonicd commented 3 years ago

thank you for the quick response.

i have installed OpenBabel via snap which installed openbabel >= 3.x.x and am installing via BiocManager which is what is being used by packrat by default on R > 3.6.0 (https://github.com/rstudio/packrat/releases)

would sessioninfo help?

yonicd commented 3 years ago

the latest Bioc version you want to install first is 3.12 that uses

do you mean ChemmineR 3.12?

on Bioc the version of ChemmineOB is 1.28.0 and the source version of ChemmineR is 3.42.0

those are the versions we are trying to install on the ubuntu machine

tgirke commented 3 years ago

Those should be fine. Next try to set the paths for OPEN_BABEL_INCDIR and OPEN_BABEL_LIBDIR as instructed in the detailed install instructions here: chrome-untrusted://terminal/html/terminal.html. This can be done within R or from the command-line.

yonicd commented 3 years ago

I looked at that INSTALL file. my headers are in /usr/lib, should the install pick that up, or do I need to be more explicit with those ENV VARS?

thanks.

tgirke commented 3 years ago

Those are specific to your system and how you installed Open Babel. For example on Debian the install (with paths) from the command-line looks like this (here after compiling Open Babel from source): R CMD INSTALL --configure-args='--with-openbabel-include=/usr/local/include/openbabel3/ --with-openbabel-lib=/usr/local/lib/openbabel/3.1.1' ChemmineOB_1.28.0.tar.gz

On Tue, Dec 22, 2020 at 8:32 AM yonicd notifications@github.com wrote:

I looked at that INSTALL file. my headers are in /usr/bin, should the install pick that up, or do I need to be more explicit with those ENV VARS?

thanks.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/girke-lab/ChemmineOB/issues/23#issuecomment-749638180, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKGMVAKDKNWR3YWUBDA27TSWDCY5ANCNFSM4MNGT6VA .

-- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521

E-mail: thomas.girke@ucr.edu URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437

yonicd commented 3 years ago

ah ok. thanks for the explicit example.

yonicd commented 3 years ago

I got a bit farther. I am getting a new error.

The installation cant find rand.h, and when i look in the paths it is indeed not there from the install using snap.

randh

Is there a specific order of installing openlabel that snap will not install all the files?

thanks again

$ echo $OPEN_BABEL_LIBDIR
/snap/openbabel/27/lib/openbabel/3.0.0
$ echo $OPEN_BABEL_INCDIR
/snap/openbabel/27/include/openbabel3
Bioconductor version 3.6 (BiocManager 1.30.10), R 3.4.4 (2018-03-15)
Installing package(s) 'BiocVersion', 'ChemmineOB'
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/ChemmineOB_1.16.2.tar.gz'
Content type 'application/x-gzip' length 1216118 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

* installing *source* package ‘ChemmineOB’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
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 how to run the C preprocessor... gcc -std=gnu99 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++  -I/usr/share/R/include -DNDEBUG  -I"/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/BH/include" -I"/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"   -I/snap/openbabel/27/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ChemmineOB.cpp -o ChemmineOB.o
ChemmineOB.cpp:1470:10: fatal error: openbabel/rand.h: No such file or directory
#include <openbabel/rand.h>
          ^~~~~~~~~~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'ChemmineOB.o' failed
make: *** [ChemmineOB.o] Error 1
ERROR: compilation failed for package ‘ChemmineOB’
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/ChemmineOB’

The downloaded source packages are in
        ‘/tmp/Rtmpvk01z1/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class,
  cluster, codetools, KernSmooth, lattice, MASS, mgcv, nlme, nnet, rpart,
  spatial, survival
Warning messages:
1: package ‘BiocVersion’ is not available (for R version 3.4.4)
2: In install.packages(...) :
  installation of package ‘ChemmineOB’ had non-zero exit status
tgirke commented 3 years ago

I don't use snap. So hard for me to help here.

Since you are on Ubuntu, try to install OpenBabel from source like:

First some dependencies you might need:

sudo apt install cmake libeigen3-dev libboost-all-dev

Clone OpenBabel 3.1.1 from GitHub here:

https://github.com/openbabel/openbabel

git clone git@github.com:openbabel/openbabel.git

mkdir build; cd build

cmake ../openbabel

make

sudo make install

On Wed, Dec 23, 2020 at 12:42 PM yonicd notifications@github.com wrote:

I got a bit farther. I am getting a new error.

The installation cant find rand.h, and when i look in the paths it is indeed not there from the install using snap.

[image: randh] https://user-images.githubusercontent.com/1755487/103035409-4483be80-4535-11eb-9922-0f664ad46eef.png

Is there a specific order of installing openlabel that snap will not install all the files?

thanks again

$ echo $OPEN_BABEL_LIBDIR

/snap/openbabel/27/lib/openbabel/3.0.0

$ echo $OPEN_BABEL_INCDIR

/snap/openbabel/27/include/openbabel3

Bioconductor version 3.6 (BiocManager 1.30.10), R 3.4.4 (2018-03-15) Installing package(s) 'BiocVersion', 'ChemmineOB' trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/ChemmineOB_1.16.2.tar.gz' Content type 'application/x-gzip' length 1216118 bytes (1.2 MB)

downloaded 1.2 MB

  • installing source package ‘ChemmineOB’ ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes 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 how to run the C preprocessor... gcc -std=gnu99 -E configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/BH/include" -I"/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I/snap/openbabel/27/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ChemmineOB.cpp -o ChemmineOB.o ChemmineOB.cpp:1470:10: fatal error: openbabel/rand.h: No such file or directory

    include <openbabel/rand.h>

      ^~~~~~~~~~~~~~~~~~

    compilation terminated. /usr/lib/R/etc/Makeconf:168: recipe for target 'ChemmineOB.o' failed make: *** [ChemmineOB.o] Error 1 ERROR: compilation failed for package ‘ChemmineOB’

  • removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/ChemmineOB’

The downloaded source packages are in

    ‘/tmp/Rtmpvk01z1/downloaded_packages’

Installation path not writeable, unable to update packages: boot, class,

cluster, codetools, KernSmooth, lattice, MASS, mgcv, nlme, nnet, rpart,

spatial, survival Warning messages: 1: package ‘BiocVersion’ is not available (for R version 3.4.4) 2: In install.packages(...) :

installation of package ‘ChemmineOB’ had non-zero exit status

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-- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521

E-mail: thomas.girke@ucr.edu URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437

yonicd commented 3 years ago

thanks. i'll try that.

yonicd commented 3 years ago

works!

i used this dockerfile in the end, with the steps you wrote

FROM rocker/r-base
RUN apt-get update && apt-get install -y cmake libeigen3-dev libboost-all-dev git
RUN git clone https://github.com/openbabel/openbabel.git
RUN mkdir build; cd build
RUN cmake ../openbabel
RUN make
RUN make install
ENV OPEN_BABEL_INCDIR=/usr/local/include/openbabel3/
ENV OPEN_BABEL_LIBDIR=usr/local/lib/openbabel/3.1.1

# ensure that the renv package cache env var is accessible in default R installation
RUN mkdir /usr/local/lib/R/etc
RUN mkdir -p /renv/cache
RUN echo "RENV_PATHS_CACHE=/renv/cache" >> /usr/local/lib/R/etc/Renviron
COPY .Rprofile /renv/.Rprofile

WORKDIR /project
RUN R -e 'install.packages(c("renv","BiocManager"))'
RUN R -e 'renv::consent(provided = TRUE)'
RUN R -e 'renv::init()'
RUN R -e "renv::install('bioc::ChemmineOB')"
tgirke commented 2 years ago

closed