I am trying to publish an app that works locally on my machine but it's failing when I publish it to shinyapps.io. My app uses a package from bioconductor: ChemmineR. I have included library(ChemmineR) in the app.R file. I have been able to publish the app to shinyapps but when I run it, the app crashes and I get the following error in the logs:
2019-10-28T15:37:39.992962+00:00 shinyapps[1237533]: ChemmineOB not found, falling back to web service version. This will be much slower
2019-10-28T15:37:40.173662+00:00 shinyapps[1237533]:
2019-10-28T15:37:40.179588+00:00 shinyapps[1237533]: 97:
2019-10-28T15:37:40.173659+00:00 shinyapps[1237533]: Warning: Error in : Forbidden
After seeing this error, I have tried to include library(ChemmineOB) in app.R but anytime I try to deploy the app online, I get another error but this time in RStudio.
[2019-10-28T15:43:18.743393908+0000] Building R package: ChemmineOB (1.22.0)
/mnt/packages/build /mnt
installing to library ‘/opt/R/3.6.1/lib/R/library’
installing source package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I"/opt/R/3.6.1/lib/R/library/BH/include" -I"/opt/R/3.6.1/lib/R/library/Rcpp/include" -I/usr/local/include -I/usr/include/eigen3 -DUSE_BOOST -fpic -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o
g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I"/opt/R/3.6.1/lib/R/library/BH/include" -I"/opt/R/3.6.1/lib/R/library/Rcpp/include" -I/usr/local/include -I/usr/include/eigen3 -DUSE_BOOST -fpic -g -O2 -c canonical.cpp -o canonical.o
canonical.cpp:2:35: fatal error: openbabel/babelconfig.h: No such file or directory
compilation terminated.
/opt/R/3.6.1/lib/R/etc/Makeconf:176: recipe for target 'canonical.o' failed
make: *** [canonical.o] Error 1
make: *** Waiting for unfinished jobs....
ChemmineOB.cpp:745:31: fatal error: openbabel/generic.h: No such file or directory
compilation terminated.
/opt/R/3.6.1/lib/R/etc/Makeconf:176: recipe for target 'ChemmineOB.o' failed
make: *** [ChemmineOB.o] Error 1
ERROR: compilation failed for package ‘ChemmineOB’
removing ‘/opt/R/3.6.1/lib/R/library/ChemmineOB’
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 662224848 failed: Error building image: Error building ChemmineOB (1.22.0). Build exited with non-zero status: 1
Execution halted
I have tried to compile the ChemmineOB from source on Windows but I'm receiving the following error when I get to the part that "For x64 builds: ... Run:
C:\openbabel\build\x64>cmake -G "Unix Makefiles" -DCMAKE_C_FLAGS=-m64 -DCMAKE_CXX_FLAGS=-m64 -DCMAKE_RC_COMPILER=c:/Rtools/mingw_64/bin/gcc.exe -DBUILD_SHARED=OFF -DCMAKE_INSTALL_PREFIX=c:/openbabel/bin/x64 -DZLIB_INCLUDE_DIR=C:/Users/kbronson/Documents/R/win-library/3.6/zlibbioc/include -DZLIB_LIBRARY=C:/Users/kbronson/Documents/R/win-library/3.6/zlibbioc/libs/x64/zlib1bioc.dll c:/openbabel/src/x64
CMake Error: The source directory "C:/openbabel/src/x64" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.
I cannot seem to get this app working on shinyapps and I would love some help. If anybody is seeing some issue I'm doing wrong or can help me get this bioconductor package working, I'd greatly appreciate it.
The output of rsconnect::appDependencies() is as follows:
I am running setRepositories(addURLs = c(BioC = "Bioconductor - 3.9 Software Packages")) each time I restart R to push the application but I'm still running into these issues.
Thanks @josh. I have submitted a pull request and I was able to get ChemmineOB to install correctly in the test.R file but I had to edit a couple other packages' test.R files because of deprecated functions being used to test the packages. My pull request was finally able to pass the Travis CI build check but I am not sure if updating all of the packages was necessary. Now that I have the bit of code that I need to install openbabel and ChemmineOB inside of the pull request, is there anything else that needs to be done additionally or differently or do I just have to wait until it is merged by somebody with write permissions to rstudio's github?
You need to wait for the pull request to be merged and subsequently deployed to production. With the holiday next week, it isn't clear when this will happen, though I will try to take a look later today.
The pull request was accepted and merged with the master branch but I still have not been able to deploy my app because it's still failing to build Bioconductor's ChemmineOB package. According to the logs, openbabel is not installed and I'm not sure what I'm missing at this point. I have tried deploying the app on a windows and ubuntu machine but they're both failing to build ChemmineOB. Below are the logs I from attempting to deploy the app:
Preparing to deploy application...DONE
Uploading bundle for application: 1237533...DONE
Deploying bundle: 2641589 for application: 1237533 ...
Waiting for task: 673243625
building: Parsing manifest
building: Building image: 2881954
building: Installing system dependencies
building: Fetching packages
building: Building package: ChemmineOB
################################ Begin Task Log ################################
[2019-12-04T20:46:35.669536680+0000] Execute script: packages/build/rJava.sh
+ set -e
+ /usr/bin/R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.8.0_212
Java home path : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c conftest.c -o conftest.o
gcc -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -o conftest.so conftest.o -L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm -L/opt/R/3.6.1/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
Updating Java configuration in /opt/R/3.6.1/lib/R
Done.
[2019-12-04T20:46:36.545825208+0000] Execute script: packages/build/sys.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libapparmor-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
libapparmor-dev
0 upgraded, 1 newly installed, 0 to remove and 106 not upgraded.
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debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libapparmor-dev:amd64.
(Reading database ... 119718 files and directories currently installed.)
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Unpacking libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
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Setting up libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
[2019-12-04T20:46:41.020323852+0000] Execute script: packages/build/rsvg.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y librsvg2-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 gir1.2-glib-2.0 gir1.2-rsvg-2.0
libgdk-pixbuf2.0-dev libgirepository-1.0-1 librsvg2-2 librsvg2-common
Suggested packages:
librsvg2-bin librsvg2-doc
The following NEW packages will be installed:
gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 gir1.2-glib-2.0 gir1.2-rsvg-2.0
libgdk-pixbuf2.0-dev libgirepository-1.0-1 librsvg2-2 librsvg2-common
librsvg2-dev
0 upgraded, 9 newly installed, 0 to remove and 106 not upgraded.
Need to get 479 kB of archives.
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Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 librsvg2-2 amd64 2.40.13-3 [93.9 kB]
Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 gir1.2-rsvg-2.0 amd64 2.40.13-3 [3690 B]
Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgdk-pixbuf2.0-dev amd64 2.32.2-1ubuntu1.6 [44.3 kB]
Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 librsvg2-common amd64 2.40.13-3 [5034 B]
Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 librsvg2-dev amd64 2.40.13-3 [103 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libgirepository-1.0-1:amd64.
(Reading database ... 119740 files and directories currently installed.)
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Unpacking librsvg2-dev:amd64 (2.40.13-3) ...
Processing triggers for libc-bin (2.23-0ubuntu11) ...
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Setting up gir1.2-glib-2.0:amd64 (1.46.0-3ubuntu1) ...
Setting up gir1.2-freedesktop:amd64 (1.46.0-3ubuntu1) ...
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Setting up librsvg2-2:amd64 (2.40.13-3) ...
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Processing triggers for libc-bin (2.23-0ubuntu11) ...
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R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> install.packages("BiocInstaller", repos="http://www.bioconductor.org/packages/3.10/bioc")
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.6.1)
>
>
[2019-12-04T20:46:48.410045091+0000] Installing R package: ClearanceTool (0.0.0.9000)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘ClearanceTool’ ...
* DONE (ClearanceTool)
[2019-12-04T20:46:48.609081853+0000] Installing R package: viridisLite (0.3.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘viridisLite’ ...
* DONE (viridisLite)
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* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘sourcetools’ ...
* DONE (sourcetools)
[2019-12-04T20:46:49.046738934+0000] Installing R package: rlang (0.4.2)
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* DONE (rlang)
[2019-12-04T20:46:49.300463783+0000] Installing R package: stringi (1.4.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘stringi’ ...
* DONE (stringi)
[2019-12-04T20:46:49.663189934+0000] Installing R package: rJava (0.9-11)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
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* DONE (rJava)
[2019-12-04T20:46:49.972723305+0000] Installing R package: sys (3.3)
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[2019-12-04T20:46:50.172807739+0000] Installing R package: fansi (0.4.0)
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* DONE (proto)
[2019-12-04T20:46:51.033738025+0000] Installing R package: Deriv (3.9.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘Deriv’ ...
* DONE (Deriv)
[2019-12-04T20:46:51.230930457+0000] Installing R package: curl (4.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘curl’ ...
* DONE (curl)
[2019-12-04T20:46:51.501920528+0000] Installing R package: ini (0.3.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘ini’ ...
* DONE (ini)
[2019-12-04T20:46:51.694596108+0000] Installing R package: whisker (0.4)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
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* DONE (whisker)
[2019-12-04T20:46:51.908564976+0000] Installing R package: base64enc (0.1-3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
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* DONE (base64enc)
[2019-12-04T20:46:52.108844131+0000] Installing R package: clipr (0.7.0)
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[2019-12-04T20:46:52.309848863+0000] Installing R package: magrittr (1.5)
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[2019-12-04T20:46:52.523386207+0000] Installing R package: colorspace (1.4-1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
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[2019-12-04T20:46:52.910838952+0000] Installing R package: png (0.1-7)
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[2019-12-04T20:46:53.112104192+0000] Installing R package: plogr (0.2.0)
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[2019-12-04T20:46:53.316647464+0000] Installing R package: fastmap (1.0.1)
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[2019-12-04T20:46:53.538752967+0000] Installing R package: munsell (0.5.0)
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[2019-12-04T20:46:53.754200688+0000] Installing R package: MASS (7.3-51.4)
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[2019-12-04T20:46:54.105296459+0000] Installing R package: neuralnet (1.44.2)
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[2019-12-04T20:46:54.302127705+0000] Installing R package: pkgconfig (2.0.3)
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[2019-12-04T20:46:54.502720875+0000] Installing R package: lattice (0.20-38)
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[2019-12-04T20:46:54.856782309+0000] Installing R package: bitops (1.0-6)
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[2019-12-04T20:46:55.053781464+0000] Installing R package: BiocGenerics (0.32.0)
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[2019-12-04T20:46:55.595865138+0000] Installing R package: Matrix (1.2-18)
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[2019-12-04T20:46:56.224541632+0000] Installing R package: askpass (1.1)
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[2019-12-04T20:46:56.423078346+0000] Installing R package: BiocManager (1.30.10)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
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[2019-12-04T20:46:56.624231945+0000] Installing R package: openssl (1.4.1)
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[2019-12-04T20:46:56.930805850+0000] Installing R package: prettyunits (1.0.2)
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[2019-12-04T20:46:57.127106044+0000] Installing R package: zlibbioc (1.32.0)
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[2019-12-04T20:46:57.328604357+0000] Installing R package: iterators (1.0.12)
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[2019-12-04T20:46:57.558089887+0000] Installing R package: itertools (0.1-3)
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* installing *binary* package ‘itertools’ ...
* DONE (itertools)
[2019-12-04T20:46:57.775613189+0000] Installing R package: mime (0.7)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘mime’ ...
* DONE (mime)
[2019-12-04T20:46:57.975215969+0000] Installing R package: gtable (0.3.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘gtable’ ...
* DONE (gtable)
[2019-12-04T20:46:58.235745391+0000] Installing R package: gridExtra (2.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘gridExtra’ ...
* DONE (gridExtra)
[2019-12-04T20:46:58.496997341+0000] Installing R package: RColorBrewer (1.1-2)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘RColorBrewer’ ...
* DONE (RColorBrewer)
[2019-12-04T20:46:58.698881788+0000] Installing R package: ellipsis (0.3.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘ellipsis’ ...
* DONE (ellipsis)
[2019-12-04T20:46:58.899290482+0000] Installing R package: digest (0.6.23)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘digest’ ...
* DONE (digest)
[2019-12-04T20:46:59.127406945+0000] Installing R package: memoise (1.1.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘memoise’ ...
* DONE (memoise)
[2019-12-04T20:46:59.323736240+0000] Installing R package: backports (1.1.5)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘backports’ ...
* DONE (backports)
[2019-12-04T20:46:59.523999696+0000] Installing R package: rprojroot (1.3-2)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘rprojroot’ ...
* DONE (rprojroot)
[2019-12-04T20:46:59.727048001+0000] Installing R package: xtable (1.8-4)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘xtable’ ...
* DONE (xtable)
[2019-12-04T20:46:59.960390846+0000] Installing R package: Rcpp (1.0.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘Rcpp’ ...
* DONE (Rcpp)
[2019-12-04T20:47:00.799061058+0000] Installing R package: plyr (1.8.4)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘plyr’ ...
* DONE (plyr)
[2019-12-04T20:47:01.048393196+0000] Installing R package: fs (1.3.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘fs’ ...
* DONE (fs)
[2019-12-04T20:47:01.339920082+0000] Installing R package: rstudioapi (0.10)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘rstudioapi’ ...
* DONE (rstudioapi)
[2019-12-04T20:47:01.564492135+0000] Installing R package: gsubfn (0.7)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘gsubfn’ ...
* DONE (gsubfn)
[2019-12-04T20:47:01.791540926+0000] Installing R package: withr (2.1.2)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘withr’ ...
* DONE (withr)
[2019-12-04T20:47:02.006573141+0000] Installing R package: nlme (3.1-142)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘nlme’ ...
* DONE (nlme)
[2019-12-04T20:47:02.408931570+0000] Installing R package: mgcv (1.8-31)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘mgcv’ ...
* DONE (mgcv)
[2019-12-04T20:47:02.815327274+0000] Installing R package: zeallot (0.1.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘zeallot’ ...
* DONE (zeallot)
[2019-12-04T20:47:03.017703763+0000] Installing R package: labeling (0.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘labeling’ ...
* DONE (labeling)
[2019-12-04T20:47:03.215919966+0000] Installing R package: htmltools (0.4.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘htmltools’ ...
* DONE (htmltools)
[2019-12-04T20:47:03.447052787+0000] Installing R package: DBI (1.0.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘DBI’ ...
* DONE (DBI)
[2019-12-04T20:47:03.712145321+0000] Installing R package: bit (1.1-14)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘bit’ ...
* DONE (bit)
[2019-12-04T20:47:03.927861456+0000] Installing R package: bit64 (0.9-7)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘bit64’ ...
* DONE (bit64)
[2019-12-04T20:47:04.161232309+0000] Installing R package: purrr (0.3.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘purrr’ ...
* DONE (purrr)
[2019-12-04T20:47:04.392784877+0000] Installing R package: fingerprint (3.5.7)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘fingerprint’ ...
* DONE (fingerprint)
[2019-12-04T20:47:04.605379740+0000] Installing R package: RCurl (1.95-4.12)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘RCurl’ ...
* DONE (RCurl)
[2019-12-04T20:47:04.898721887+0000] Installing R package: clisymbols (1.2.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘clisymbols’ ...
* DONE (clisymbols)
[2019-12-04T20:47:05.095912196+0000] Installing R package: R6 (2.4.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘R6’ ...
* DONE (R6)
[2019-12-04T20:47:05.296092493+0000] Installing R package: chron (2.3-54)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘chron’ ...
* DONE (chron)
[2019-12-04T20:47:05.500889731+0000] Installing R package: yaml (2.2.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘yaml’ ...
* DONE (yaml)
[2019-12-04T20:47:05.726748825+0000] Installing R package: lazyeval (0.2.2)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘lazyeval’ ...
* DONE (lazyeval)
[2019-12-04T20:47:05.947053834+0000] Installing R package: rsvg (1.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘rsvg’ ...
* DONE (rsvg)
[2019-12-04T20:47:06.146467794+0000] Installing R package: glue (1.3.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘glue’ ...
* DONE (glue)
[2019-12-04T20:47:06.365676724+0000] Installing R package: vctrs (0.2.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘vctrs’ ...
* DONE (vctrs)
[2019-12-04T20:47:06.627273729+0000] Installing R package: blob (1.2.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘blob’ ...
* DONE (blob)
[2019-12-04T20:47:06.826207560+0000] Installing R package: hms (0.5.2)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘hms’ ...
* DONE (hms)
[2019-12-04T20:47:07.031217231+0000] Installing R package: tidyselect (0.2.5)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘tidyselect’ ...
* DONE (tidyselect)
[2019-12-04T20:47:07.269224343+0000] Installing R package: stringr (1.4.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘stringr’ ...
* DONE (stringr)
[2019-12-04T20:47:07.494431312+0000] Installing R package: reshape2 (1.4.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘reshape2’ ...
* DONE (reshape2)
[2019-12-04T20:47:07.738092358+0000] Installing R package: lifecycle (0.1.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘lifecycle’ ...
* DONE (lifecycle)
[2019-12-04T20:47:07.955199478+0000] Installing R package: scales (1.1.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘scales’ ...
* DONE (scales)
[2019-12-04T20:47:08.184510695+0000] Installing R package: jsonlite (1.6)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘jsonlite’ ...
* DONE (jsonlite)
[2019-12-04T20:47:08.466521815+0000] Installing R package: httr (1.4.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘httr’ ...
* DONE (httr)
[2019-12-04T20:47:08.702368653+0000] Installing R package: htmlwidgets (1.5.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘htmlwidgets’ ...
* DONE (htmlwidgets)
[2019-12-04T20:47:08.973043426+0000] Installing R package: gh (1.0.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘gh’ ...
* DONE (gh)
[2019-12-04T20:47:09.172198205+0000] Installing R package: FNN (1.1.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘FNN’ ...
* DONE (FNN)
[2019-12-04T20:47:09.398777226+0000] Installing R package: rcdklibs (2.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘rcdklibs’ ...
* DONE (rcdklibs)
[2019-12-04T20:47:10.222662565+0000] Installing R package: rcdk (3.4.7.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘rcdk’ ...
* DONE (rcdk)
[2019-12-04T20:47:10.450770349+0000] Installing R package: crayon (1.3.4)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘crayon’ ...
* DONE (crayon)
[2019-12-04T20:47:10.677792740+0000] Installing R package: cli (1.1.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘cli’ ...
* DONE (cli)
[2019-12-04T20:47:10.884142027+0000] Installing R package: pillar (1.4.2)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘pillar’ ...
* DONE (pillar)
[2019-12-04T20:47:11.096379125+0000] Installing R package: tibble (2.1.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘tibble’ ...
* DONE (tibble)
[2019-12-04T20:47:11.325672085+0000] Installing R package: ggplot2 (3.2.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘ggplot2’ ...
* DONE (ggplot2)
[2019-12-04T20:47:11.715520638+0000] Installing R package: desc (1.2.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘desc’ ...
* DONE (desc)
[2019-12-04T20:47:11.929816026+0000] Installing R package: BH (1.69.0-1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘BH’ ...
* DONE (BH)
[2019-12-04T20:47:22.107748872+0000] Installing R package: dplyr (0.8.3)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘dplyr’ ...
* DONE (dplyr)
[2019-12-04T20:47:23.155738731+0000] Installing R package: later (1.0.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘later’ ...
* DONE (later)
[2019-12-04T20:47:23.424853353+0000] Installing R package: promises (1.1.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘promises’ ...
* DONE (promises)
[2019-12-04T20:47:23.709344484+0000] Installing R package: httpuv (1.5.2)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘httpuv’ ...
* DONE (httpuv)
[2019-12-04T20:47:24.214127834+0000] Installing R package: shiny (1.4.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘shiny’ ...
* DONE (shiny)
[2019-12-04T20:47:24.825922193+0000] Installing R package: miniUI (0.1.1.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘miniUI’ ...
* DONE (miniUI)
[2019-12-04T20:47:25.022918833+0000] Installing R package: chemdoodle (0.3.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘chemdoodle’ ...
* DONE (chemdoodle)
[2019-12-04T20:47:25.277043288+0000] Installing R package: shinyBS (0.61)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘shinyBS’ ...
* DONE (shinyBS)
[2019-12-04T20:47:25.494957827+0000] Installing R package: shinyjs (1.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘shinyjs’ ...
* DONE (shinyjs)
[2019-12-04T20:47:25.758487527+0000] Installing R package: shinydashboard (0.7.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘shinydashboard’ ...
* DONE (shinydashboard)
[2019-12-04T20:47:25.995280122+0000] Installing R package: shinydashboardPlus (0.7.0)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘shinydashboardPlus’ ...
* DONE (shinydashboardPlus)
[2019-12-04T20:47:26.340665082+0000] Installing R package: readr (1.3.1)
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *binary* package ‘readr’ ...
* DONE (readr)
[2019-12-04T20:47:26.933560833+0000] Building R package: ChemmineOB (1.24.0)
/mnt/packages/build /mnt
* installing to library ‘/opt/R/3.6.1/lib/R/library’
* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I"/opt/R/3.6.1/lib/R/library/BH/include" -I"/opt/R/3.6.1/lib/R/library/Rcpp/include" -I/usr/local/include -I/usr/include/eigen3 -DUSE_BOOST -fpic -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o
g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I"/opt/R/3.6.1/lib/R/library/BH/include" -I"/opt/R/3.6.1/lib/R/library/Rcpp/include" -I/usr/local/include -I/usr/include/eigen3 -DUSE_BOOST -fpic -g -O2 -c canonical.cpp -o canonical.o
canonical.cpp:2:35: fatal error: openbabel/babelconfig.h: No such file or directory
compilation terminated.
/opt/R/3.6.1/lib/R/etc/Makeconf:176: recipe for target 'canonical.o' failed
make: *** [canonical.o] Error 1
make: *** Waiting for unfinished jobs....
ChemmineOB.cpp:745:31: fatal error: openbabel/generic.h: No such file or directory
compilation terminated.
/opt/R/3.6.1/lib/R/etc/Makeconf:176: recipe for target 'ChemmineOB.o' failed
make: *** [ChemmineOB.o] Error 1
ERROR: compilation failed for package ‘ChemmineOB’
* removing ‘/opt/R/3.6.1/lib/R/library/ChemmineOB’
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 673243628 failed: Error building image: Error building ChemmineOB (1.24.0). Build exited with non-zero status: 1
Execution halted
We have been attempting to clear out the backlog of PR's and issues, sadly new ones keep cropping up and that has prevented getting this out to production. Once in production, we will attempt to ping the issues, PRs and Community posts that have interest. Thank you for bearing with us.