├── .gitignore
├── Makefile
├── README.md
├── docker-lambdar
    ├── Dockerfile
    └── README.md
├── lambdar.js
├── lambdar.mk
└── test-r.sh


/.gitignore:
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1 | *~
2 | lambdar.zip
3 | lambdar.zip*.json
4 | r-*.tar.gz
5 | r/
6 | test-r-interactive.sh
7 | .Rhistory
8 | 


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/Makefile:
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 1 | # Lambdar: Build R for Amazon Linux and deploy to AWS Lambda
 2 | #
 3 | # Usage:
 4 | #  make docker   - build AWS Lambda compatible R Docker container
 5 | #  make lambdar  - build minimal r-$(R_VERSION).tar.gz for AWS Lambda
 6 | #  make test     - quick check that the built R version works
 7 | #  make create   - Create AWS Lambda function from local ZIP file
 8 | #  make deploy   - Update AWS Lambda function from local ZIP file
 9 | #
10 | # The Docker container henrikbengtsson/lambdar:build is defined by
11 | # the docker-lambdar/Dockerfile file.
12 | name=lambdar
13 | 
14 | R_VERSION=3.5.0
15 | 
16 | # R must be built on a system compatible with Amazon Linux with glibc <= 2.17.
17 | glibc_version=$(shell ldd --version | head -1 | sed -E 's/.*GLIBC[[:space:]]([0-9.-]+).*/\1/g' | tr - .)
18 | glibc_version_smallest=$(shell printf "$(glibc_version)\n2.17" | sort -V | head -1)
19 | #ifeq ($(glibc_version_smallest), 2.17)
20 | #  $(error "ERROR: R must be built with GLIBC (<= 2.17) in order to work on AWS Lambda: $(glibc_version)")
21 | #endif
22 | 
23 | .DELETE_ON_ERROR:
24 | .SECONDARY:
25 | 
26 | all: docker lambdar
27 | 
28 | lambdar: $(name).zip
29 | 
30 | docker:
31 | 	docker build -t henrikbengtsson/lambdar:build docker-lambdar/
32 | 
33 | debug:
34 | 	@echo "R version: $(R_VERSION)"
35 | 	@echo "GLIBC version: $(glibc_version)"
36 | 
37 | create: $(name).zip.create.json
38 | 
39 | deploy: $(name).zip.deploy.json
40 | 
41 | # Bundle up R and all of its dependencies
42 | r-%.tar.gz: lambdar.mk
43 | 	docker run -v $(PWD):/xfer -w /xfer henrikbengtsson/lambdar:build make -f lambdar.mk
44 | 
45 | test: r-$(R_VERSION).tar.gz
46 | 	docker run -it --env INTERACTIVE=true --env R_VERSION=$(R_VERSION) -v $(PWD):/xfer -w /xfer henrikbengtsson/lambdar:build bash -C test-r.sh
47 | 
48 | # Build the zip archive for AWS Lambda
49 | %.zip: %.js r-$(R_VERSION).tar.gz
50 | 	zip -qr $@ $^
51 | 
52 | # Create Lambda function from local ZIP (function name must not contain periods)
53 | # Required environment variables:
54 | # * AWS_LAMBDA_ROLE_ARN ="arn:aws:iam::<digits>:role/service-role/<name>"
55 | %.zip.create.json: %.zip
56 | aws lambda create-function --runtime nodejs8.10 --handler $*.handler --timeout 10 --role $$AWS_LAMBDA_ROLE_ARN --function-name $*-$(subst .,_,$(R_VERSION)) --description "R $(R_VERSION)" --zip-file fileb://$< > $@
57 | 
58 | # Update the Lambda function from local ZIP
59 | %.zip.deploy.json: %.zip
60 | 	aws lambda update-function-code --function-name $*-$(subst .,_,$(R_VERSION)) --zip-file fileb://$< > $@
61 | 
62 | clean:
63 | 	@rm -f r-$(R_VERSION).tar.gz
64 | 	@rm -f $(name).zip
65 | 


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/README.md:
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 1 | # ƛR: Lambdar
 2 | 
 3 | Run R on AWS Lambda.
 4 | 
 5 | # tl;dr
 6 | 
 7 | <http://lambdar.sjackman.ca/?e=stem(rnorm(100))>
 8 | 
 9 | ```
10 |   The decimal point is at the |
11 | 
12 |   -2 | 3
13 |   -1 | 87666
14 |   -1 | 333332210
15 |   -0 | 999988888655
16 |   -0 | 444433333222222111110
17 |    0 | 00001111111112223344
18 |    0 | 5556667777889999
19 |    1 | 00111123344
20 |    1 | 556
21 |    2 | 14
22 | ```
23 | 
24 | # Code
25 | 
26 | See the Lambda function [lambdar.js](lambdar.js) and [Makefile](Makefile).
27 | 
28 | # API Examples
29 | 
30 | ### HTTP GET
31 | 
32 | ```
33 | ❯❯❯ curl -L 'http://lambdar.sjackman.ca/?e=355/113'
34 | [1] 3.141593
35 | ```
36 | 
37 | ```
38 | ❯❯❯ curl 'https://8nhzfyyq66.execute-api.us-west-2.amazonaws.com/prod/lambdar?e=355/113'
39 | [1] 3.141593
40 | ```
41 | 
42 | ### HTTP PUT
43 | 
44 | ```
45 | ❯❯❯ curl -d '355/113' https://8nhzfyyq66.execute-api.us-west-2.amazonaws.com/prod/lambdar
46 | [1] 3.141593
47 | ```
48 | 
49 | Sadly, HTTP PUT does not work with the redirected URL <http://lambdar.sjackman.ca>.
50 | 


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/docker-lambdar/Dockerfile:
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 1 | ## Build usage:
 2 | ##  docker build -t henrikbengtsson/lambdar:build .
 3 | ##
 4 | ## Run usage:
 5 | ##  docker run -i -t henrikbengtsson/lambdar:build bash
 6 | ##
 7 | ## Source: https://github.com/{HenrikBengtsson|sjackman}/lambdar
 8 | ## Copyright: Henrik Bengtsson (2017-2018)
 9 | ## License: GPL (>= 2.1) [https://www.gnu.org/licenses/gpl.html]
10 | 
11 | FROM lambci/lambda:build
12 | 
13 | MAINTAINER Henrik Bengtsson "henrikb@braju.com"
14 | 
15 | RUN yum install -y gcc-gfortran
16 | RUN yum install -y libgfortran     # Otherwise ld error duing 'make'
17 | RUN yum install -y readline-devel  # Required iff --with-readline=yes
18 | RUN yum install -y bzip2-devel
19 | RUN yum install -y xz-devel        # liblzma
20 | RUN yum install -y pcre-devel
21 | RUN yum install -y curl-devel
22 | 
23 | ## Optional
24 | RUN yum install -y libpng-devel
25 | 
26 | ENV R_VERSION=3.5.0
27 | ENV R_READLINE=yes
28 | ENV R_PREFIX=/tmp/r-local/${R_VERSION}
29 | 
30 | ## Build and install R from source
31 | RUN cd /tmp; curl -O https://cloud.r-project.org/src/base/R-3/R-${R_VERSION}.tar.gz
32 | RUN cd /tmp; tar -zxf R-${R_VERSION}.tar.gz
33 | RUN cd /tmp/R-${R_VERSION}; ./configure --with-readline=${R_READLINE} --without-x --without-libtiff --without-jpeglib --without-cairo --without-lapack --without-ICU --without-recommended-packages --disable-R-profiling --disable-java --disable-nls --prefix=${R_PREFIX}
34 | RUN cd /tmp/R-${R_VERSION}; make
35 | RUN cd /tmp/R-${R_VERSION}; make install
36 | 
37 | ## R runtime properties
38 | RUN mkdir ${R_PREFIX}/lib64/R/site-library  ## Where to install packages
39 | 
40 | ENV PATH=${R_PREFIX}/bin:${PATH}
41 | ENV R_BIOC_VERSION=3.7
42 | RUN echo "R_BIOC_VERSION=${R_BIOC_VERSION}" >> ~/.Renviron
43 | RUN echo "options(repos = c(CRAN='https://cloud.r-project.org', BioCsoft='https://bioconductor.org/packages/${R_BIOC_VERSION}/bioc', BioCann='https://bioconductor.org/packages/${R_BIOC_VERSION}/data/annotation', BioCexp='https://bioconductor.org/packages/${R_BIOC_VERSION}/data/experiment'))" >> ~/.Rprofile
44 | 


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/docker-lambdar/README.md:
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 1 | # Short Description
 2 | 
 3 | Amazon AWS Lambda environment extended with a build environment containing a minimalistic R
 4 | 
 5 | 
 6 | # Full Description
 7 | 
 8 | The [lambci/lambda](https://hub.docker.com/r/lambci/lambda/) images reproduce the Amazon AWS Lambda environment as far as possible.  This image ([Dockerfile](https://github.com/HenrikBengtsson/lambdar)) extends their `lambci/lambda:build` image by providing a minimalistic [R](https://www.r-project.org/) installation.
 9 | 
10 | Note that this is a _build environment_ containing a minimalistic R installation.  It requires more work in order to deploy the R software on AWS Lambda.
11 | 


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/lambdar.js:
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 1 | 'use strict';
 2 | 
 3 | const fs = require('fs');
 4 | const spawnSync = require('child_process').spawnSync;
 5 | 
 6 | /** The version of R */
 7 | const version = '3.5.0';
 8 | 
 9 | function spawn(command, args) {
10 |     const output = spawnSync(command, args, {
11 |         env: {
12 |             HOME: process.cwd(),
13 |             LD_LIBRARY_PATH: '/tmp/r/${version}/lib64/R/lib'
14 |         }
15 |     });
16 |     if (output.error != null) {
17 |         console.log(output);
18 |         return output.error.toString();
19 |     }
20 |     const s = output.stdout.toString() + output.stderr.toString();
21 |     console.log(s);
22 |     return s;
23 | }
24 | 
25 | function install_r() {
26 |     if (fs.existsSync('/tmp/r'))
27 |         return;
28 |     spawn('tar', ['xf', `/var/task/r-${version}.tar.gz`, '-C', '/tmp']);
29 | }
30 | 
31 | function chdir_home() {
32 |     const path = `/tmp/${process.pid}.${Math.random()}`;
33 |     fs.mkdirSync(path);
34 |     process.env.HOME = path;
35 |     process.chdir(path);
36 | }
37 | 
38 | function eval_r(expr) {
39 |     chdir_home();
40 |     return spawn(`/tmp/r/${version}/bin/Rscript`, ['-e', expr])
41 | }
42 | 
43 | /**
44 |  * Transfer bottles from CircleCI to BinTray and GitHub
45 |  */
46 | exports.handler = (event, context, callback) => {
47 |     console.log('Received event:', JSON.stringify(event, null, 2));
48 | 
49 |     const done = (err, res) => callback(null, {
50 |         statusCode: err ? '400' : '200',
51 |         body: err ? err.message : res,
52 |         headers: {
53 |             'Content-Type': 'text/plain',
54 |         },
55 |     });
56 | 
57 |     const redirect = (url) => callback(null, {
58 |         statusCode: 303,
59 |         headers: { 'Content-Type': 'text/html', 'Location': url },
60 |         body: `<html><body>You are being <a href="${url}">redirected</a>.</body></html>`
61 |     });
62 | 
63 |     switch (event.httpMethod) {
64 |         case 'GET':
65 |             if (event.queryStringParameters == null || !('e' in event.queryStringParameters)) {
66 |                 redirect('https://github.com/sjackman/lambdar');
67 |                 break;
68 |             }
69 |         case 'POST':
70 |             const expr = event.httpMethod == "GET" ? event.queryStringParameters.e : event.body;
71 |             console.log(expr);
72 |             install_r();
73 |             done(null, eval_r(expr));
74 |             break;
75 |         default:
76 |             done(new Error(`lambdar: Unsupported HTTP method "${event.httpMethod}"`));
77 |     }
78 | };
79 | 


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/lambdar.mk:
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 1 | # lambdar: Build R to run on AWS Lambda
 2 | 
 3 | R_VERSION=3.5.0
 4 | R_REPOS=https://cloud.r-project.org
 5 | 
 6 | R_PREFIX=/tmp/r/$(R_VERSION)
 7 | 
 8 | .DELETE_ON_ERROR:
 9 | .SECONDARY:
10 | 
11 | all: r-$(R_VERSION).tar.gz
12 | 
13 | # Build R from source
14 | /tmp/r/%: /tmp/R-%
15 | 	cd /tmp/R-$*;\
16 | 	./configure --with-readline=${R_READLINE} --without-x --without-libtiff --without-jpeglib --without-cairo --without-lapack --without-ICU --without-recommended-packages --disable-R-profiling --disable-java --disable-nls --prefix=${R_PREFIX}; \
17 | 	make; \
18 | 	make install
19 | 
20 | # Install custom packages here, if any
21 | pkgs: /tmp/r/$(R_VERSION)
22 | #	$(R_PREFIX)/bin/Rscript -e "install.packages(c('future'), repos ='$(R_REPOS)')"
23 | 
24 | prune: /tmp/r/$(R_VERSION)
25 | 	@rm -rf $(R_PREFIX)/share
26 | 	@rm -f $(R_PREFIX)/lib64/R/COPYING $(R_PREFIX)/lib64/R/SVN-REVISION
27 | 	@rm -rf $(R_PREFIX)/lib64/R/doc/*
28 | 	@mkdir -p /tmp/r/$(R_VERSION)/lib64/R/doc/html ## install.packages()
29 | 	@rm -f $(R_PREFIX)/lib64/R/doc/NEWS*
30 | 	@rm -rf $(R_PREFIX)/lib64/R/doc/manual*
31 | 	@rm -rf $(R_PREFIX)/lib64/R/doc
32 | 	@rm -rf $(R_PREFIX)/lib64/R/share/licenses/
33 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/INDEX
34 | 	@rm -rf $(R_PREFIX)/lib64/R/library/*/demo
35 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/Meta/demo.rds
36 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/Meta/hsearch.rds
37 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/Meta/links.rds
38 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/Meta/Rd.rds
39 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/Meta/vignette.rds
40 | 	@rm -rf $(R_PREFIX)/lib64/R/library/*/doc
41 | 	@rm -rf $(R_PREFIX)/lib64/R/library/*/html
42 | 	@rm -rf $(R_PREFIX)/lib64/R/library/*/help
43 | 	@rm -rf $(R_PREFIX)/lib64/R/library/translations
44 | 	@ln -sf $(R_PREFIX)/lib64/R/bin/R $(R_PREFIX)/bin/R
45 | 	@ln -sf $(R_PREFIX)/lib64/R/bin/Rscript $(R_PREFIX)/bin/Rscript
46 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/GPL*
47 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/NEWS*
48 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/CHANGELOG*
49 | 	@rm -f $(R_PREFIX)/lib64/R/library/*/README*
50 | 	@rm -rf $(R_PREFIX)/lib64/R/library/*/vignettes*
51 | 
52 | 
53 | # Copy dependencies from amazonlinux-minimal-r build
54 | lib/%: /tmp/r/$(R_VERSION)
55 | 	cp $(shell ldconfig -p | grep $(@F) | sed 's|.*=> ||g') $(R_PREFIX)/lib64/R/lib
56 | 
57 | # Build the tarball of R and all of its dependencies
58 | r-%.tar.gz: /tmp/r/% lib/libgfortran.so.3 lib/libquadmath.so.0 lib/libgomp.so.1 pkgs prune
59 | 	tar zcf $@ -C /tmp r/$*
60 | 
61 | clean:
62 | 	@rm -rf $(R_PREFIX)
63 | 


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/test-r.sh:
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 1 | tar xf r-${R_VERSION}.tar.gz -C /tmp
 2 | export PATH=/tmp/r/${R_VERSION}/bin:${PATH}
 3 | export LD_LIBRARY_PATH=/tmp/r/${R_VERSION}/lib64/R/lib
 4 | Rscript -e "cat('R.home():', R.home(), '\n')"
 5 | Rscript -e "sessionInfo()"
 6 | if [[ ${INTERACTIVE} == "true" ]]; then
 7 |     export R_BIOC_VERSION=3.4
 8 |     mkdir /tmp/test
 9 |     cd /tmp/test
10 |     echo "R_BIOC_VERSION=${R_BIOC_VERSION}" >> .Renviron
11 |     echo "options(repos = c(CRAN='https://cloud.r-project.org', BioCsoft='https://bioconductor.org/packages/${R_BIOC_VERSION}/bioc', BioCann='https://bioconductor.org/packages/${R_BIOC_VERSION}/data/annotation', BioCexp='https://bioconductor.org/packages/${R_BIOC_VERSION}/data/experiment', BioCextra='https://bioconductor.org/packages/${R_BIOC_VERSION}/extra'))" >> .Rprofile
12 |     bash;
13 | fi
14 | 


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